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https://github.com/msberends/AMR.git
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Built site for AMR: 1.8.2.9120@68abb00
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="">1.8.2.9119</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9120</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] I R R R R I S R S R</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] S R I S S I S R S 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] -1.1618950 0.7745967 0.7745967 0.7745967 0.7745967 -1.1618950</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -1.1618950 0.7745967 -1.1618950 0.7745967</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.4743416 1.8973666 -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-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 0.01 32 128 4 0.5 <=0.005 <=0.005 0.125 </span>
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<span class="r-out co"><span class="r-pr">#></span> [10] 0.125 </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] >=256 32 8 0.005 0.002 16 16 4 0.125 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">mic</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.94388242 -1.02867586 1.12920607 1.49985337 0.57323512 0.01726417</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -1.21399951 -1.21399951 -0.35338313 -0.35338313</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 1.3250871 0.7850408 0.4250100 -1.4910484 -1.7290159 0.6050254</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.6050254 0.2449945 -0.6550826 -0.1150363</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] 0.94388242 -1.02867586 1.12920607 1.49985337 0.57323512 0.01726417</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -1.21399951 -1.21399951 -0.35338313 -0.35338313</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 1.3250871 0.7850408 0.4250100 -1.4910484 -1.7290159 0.6050254</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.6050254 0.2449945 -0.6550826 -0.1150363</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] 24 40 44 31 40 34 22 41 49 40</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 50 49 21 41 42 7 13 6 10 29</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] -1.4460560 0.4048957 0.8676336 -0.6362647 0.4048957 -0.2892112</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -1.6774250 0.5205802 1.4460560 0.4048957</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 1.3154103 1.2587116 -0.3288526 0.8051218 0.8618206 -1.1226347</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.7824423 -1.1793334 -0.9525385 0.1247372</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 R 21 2 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B R 20 2 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C S 22 1 16</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D S 28 2 16</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E I 22 1 0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F R 18 2 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G R 23 2 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H S 25 1 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I I 21 2 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J I 18 2 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 R 22 0.25 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B I 26 2 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C I 27 4 16</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D R 30 0.25 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E S 17 2 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F I 30 2 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G S 19 0.5 16</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H I 23 0.25 <=0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I R 27 1 <=0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J I 31 4 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" and</span>
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<span class="r-msg co"><span class="r-pr">#></span> "tobr"</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.14721958 0.32396692 -0.25487609 0.75483654 -1.03119985 0.15991243</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.69943595 -0.52634353 -0.07812875 -0.19482320</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.07399410 -0.03958601 0.56084503 0.09513514 -0.24454184 0.30038844</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.31486005 -0.91854813 0.11340013 0.37377319</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" and</span>
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<span class="r-msg co"><span class="r-pr">#></span> "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 22 1 16 -0.25487609 0.0000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 J I 18 2 8 -0.19482320 0.0600529</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 I I 21 2 4 -0.07812875 0.1767473</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 H S 25 1 1 -0.52634353 0.2714674</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 A R 21 2 1 0.14721958 0.4020957</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F R 18 2 4 0.15991243 0.4147885</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 B R 20 2 4 0.32396692 0.5788430</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 E I 22 1 0.25 -1.03119985 0.7763238</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 G R 23 2 8 0.69943595 0.9543120</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 D S 28 2 16 0.75483654 1.0097126</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 27 4 16 0.56084503 0.0000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 J I 31 4 2 0.37377319 0.1870718</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 F I 30 2 4 0.30038844 0.2604566</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 I R 27 1 <=0.5 0.11340013 0.4474449</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 D R 30 0.25 1 0.09513514 0.4657099</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 A R 22 0.25 8 0.07399410 0.4868509</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 B I 26 2 2 -0.03958601 0.6004310</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 E S 17 2 8 -0.24454184 0.8053869</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 G S 19 0.5 16 -0.31486005 0.8757051</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 H I 23 0.25 <=0.5 -0.91854813 1.4793932</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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