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Built site for AMR: 2.0.0@dee675e
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="">1.8.2.9152</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</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 +201,30 @@
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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 R S R S S R I R R</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] R R S I R S R R S 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] 0.7745967 0.7745967 -1.1618950 0.7745967 -1.1618950 -1.1618950</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.7745967 -1.1618950 0.7745967 0.7745967</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.7745967 0.7745967 -1.1618950 -1.1618950 0.7745967 -1.1618950</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] 0.125 0.005 16 32 0.01 <=0.001 0.01 1 0.5 </span>
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<span class="r-out co"><span class="r-pr">#></span> [10] 4 </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.002 0.002 256 0.0625 0.01 0.025 0.002 2 4 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] -0.1172241 -1.0092500 1.2273872 1.4194745 -0.8171627 -1.4552630</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.8171627 0.4590379 0.2669505 0.8432125</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.867240328 -0.867240328 2.066590798 -0.008525384 -0.465717781</span>
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<span class="r-out co"><span class="r-pr">#></span> [6] -0.237121583 -0.867240328 0.856106358 1.029032707 -0.638644130</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] -0.1172241 -1.0092500 1.2273872 1.4194745 -0.8171627 -1.4552630</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.8171627 0.4590379 0.2669505 0.8432125</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.867240328 -0.867240328 2.066590798 -0.008525384 -0.465717781</span>
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<span class="r-out co"><span class="r-pr">#></span> [6] -0.237121583 -0.867240328 0.856106358 1.029032707 -0.638644130</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] 38 45 6 20 43 49 29 31 39 33</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 42 21 42 39 44 36 46 41 9 48</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] 0.36674754 0.91296727 -2.13025696 -1.03781749 0.75690449 1.22509283</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.33553498 -0.17947220 0.44477893 -0.02340942</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.42276578 -1.28455756 0.42276578 0.17886245 0.58536800 -0.06504089</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.74797023 0.34146467 -2.26017090 0.91057245</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 +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 24 8 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B R 21 8 16</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C I 28 1 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D S 24 4 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E S 17 16 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F S 17 2 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G I 23 16 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H R 19 16 0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I R 20 0.5 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J I 27 16 8</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 27 4 <=1</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B R 20 1 <=1</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C R 31 <=0.5 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D S 23 4 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E R 31 2 <=1</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F R 24 <=0.5 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G R 28 1 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H R 22 4 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I S 23 8 <=1</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J S 26 4 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] -0.216474562 0.698891501 -0.010082051 -0.234063901 -0.060228857</span>
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<span class="r-out co"><span class="r-pr">#></span> [6] -0.586746706 -0.145237897 -0.005286713 -0.028443276 0.587672462</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.2706405 -0.6068529 0.2354050 -0.2518529 0.3034383 -0.2313769</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.4976524 0.4511070 -0.3605963 0.2337166</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 +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",</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 I 28 1 4 -0.010082051 0.000000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 H R 19 16 0.25 -0.005286713 0.004795338</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 I R 20 0.5 8 -0.028443276 0.018361225</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 E S 17 16 8 -0.060228857 0.050146806</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 G I 23 16 0.5 -0.145237897 0.135155846</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 A S 24 8 0.5 -0.216474562 0.206392511</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 D S 24 4 1 -0.234063901 0.223981850</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 F S 17 2 4 -0.586746706 0.576664654</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 J I 27 16 8 0.587672462 0.597754514</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 B R 21 8 16 0.698891501 0.708973552</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 31 <=0.5 2 0.2354050 0.00000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 J S 26 4 4 0.2337166 0.00168838</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 E R 31 2 <=1 0.3034383 0.06803327</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 H R 22 4 4 0.4511070 0.21570200</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 G R 28 1 4 0.4976524 0.26224741</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F R 24 <=0.5 2 -0.2313769 0.46678194</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 D S 23 4 2 -0.2518529 0.48725790</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 A S 27 4 <=1 -0.2706405 0.50604549</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I S 23 8 <=1 -0.3605963 0.59600133</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 B R 20 1 <=1 -0.6068529 0.84225790</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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