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Built site for AMR: 2.0.0.9003@c28cfa3
This commit is contained in:
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@@ -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="">2.0.0.9002</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9003</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] R I I R S I I I S R</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] S S I I S R R 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] 1.449138 -0.621059 -0.621059 1.449138 -0.621059 -0.621059 -0.621059</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] -0.621059 -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] 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] 2 0.0625 0.5 <=0.025 1 <=0.025 2 0.5 <=0.025</span>
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<span class="r-out co"><span class="r-pr">#></span> [10] >=256 </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.5 0.002 <=0.001 0.025 0.0625 0.25 <=0.001 64 >=256 </span>
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<span class="r-out co"><span class="r-pr">#></span> [10] 32 </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] 0.52989759 -0.67629105 0.04742213 -0.99518998 0.28865986 -0.99518998</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.52989759 0.04742213 -0.99518998 2.21856169</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.18238584 -1.00659270 -1.15585340 -0.46270817 -0.26539626 0.03312514</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -1.15585340 1.22721075 1.52573215 1.07795004</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] 0.52989759 -0.67629105 0.04742213 -0.99518998 0.28865986 -0.99518998</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.52989759 0.04742213 -0.99518998 2.21856169</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.18238584 -1.00659270 -1.15585340 -0.46270817 -0.26539626 0.03312514</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -1.15585340 1.22721075 1.52573215 1.07795004</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] 36 41 38 14 14 46 22 45 45 40</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 20 27 47 48 29 33 49 6 11 50</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] 0.1504749 0.5464614 0.3088695 -1.5918660 -1.5918660 0.9424480</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.9582875 0.8632507 0.8632507 0.4672641</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.73638265 -0.30682611 0.92047832 0.98184354 -0.18409566 0.06136522</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 1.04320876 -1.59549575 -1.28866965 1.10457398</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 30 8 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B S 30 2 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C R 27 8 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D I 17 <=1 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E I 28 <=1 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F R 27 4 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G I 25 4 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H S 19 4 0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I I 18 <=1 0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J S 26 2 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 R 30 >=16 <=0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B S 30 4 >=4</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C S 17 >=16 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D I 18 8 >=4</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E R 18 4 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F S 27 >=16 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G S 24 >=16 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H I 17 >=16 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I I 28 4 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J I 18 >=16 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] 0.51643016 -0.02872404 1.19466519 -0.54741122 -0.34374818 0.98167950</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.28671398 -0.61531550 -1.09230611 -0.35198377</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.62894141 0.21607485 -0.36363778 -0.05249015 -0.25341632 0.07976901</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.30030036 -0.01008439 -0.40293659 -0.14252040</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 27 8 8 1.19466519 0.0000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 F R 27 4 8 0.98167950 0.2129857</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 A S 30 8 2 0.51643016 0.6782350</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 G I 25 4 8 0.28671398 0.9079512</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 B S 30 2 1 -0.02872404 1.2233892</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 E I 28 <=1 1 -0.34374818 1.5384134</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 J S 26 2 0.5 -0.35198377 1.5466490</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 D I 17 <=1 8 -0.54741122 1.7420764</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 H S 19 4 0.25 -0.61531550 1.8099807</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 I I 18 <=1 0.25 -1.09230611 2.2869713</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 17 >=16 0.5 -0.36363778 0.00000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 I I 28 4 0.5 -0.40293659 0.03929881</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 E R 18 4 0.5 -0.25341632 0.11022146</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 J I 18 >=16 1 -0.14252040 0.22111737</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 D I 18 8 >=4 -0.05249015 0.31114763</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 H I 17 >=16 2 -0.01008439 0.35355339</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 F S 27 >=16 0.5 0.07976901 0.44340679</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 B S 30 4 >=4 0.21607485 0.57971263</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 G S 24 >=16 2 0.30030036 0.66393814</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 A R 30 >=16 <=0.25 0.62894141 0.99257919</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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