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Built site for AMR: 1.8.2.9101@7b00b4f
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="">1.8.2.9100</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9101</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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@ -196,31 +196,30 @@
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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] S I R I R S I I S S</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] I I I I R S 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] -0.4743416 -0.4743416 1.8973666 -0.4743416 1.8973666 -0.4743416</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.4743416 -0.4743416 -0.4743416 -0.4743416</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.4743416 -0.4743416 -0.4743416 -0.4743416 1.8973666 -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] 2 0.5 32 0.025 <=0.005 <=0.005 1 0.01 0.025 </span>
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<span class="r-out co"><span class="r-pr">#></span> [10] 0.01 </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 4 8 0.001 1 0.025 0.01 64 1 0.25 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] 1.0124233 0.5545130 1.9282440 -0.4350148 -0.9666323 -0.9666323</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.7834682 -0.7376771 -0.4350148 -0.7376771</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.6000773 0.8005604 -1.7988600 0.1991111 -0.8678454 -1.1328696</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 1.4020096 0.1991111 -0.2018550 0.8005604</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] 1.0124233 0.5545130 1.9282440 -0.4350148 -0.9666323 -0.9666323</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.7834682 -0.7376771 -0.4350148 -0.7376771</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.6000773 0.8005604 -1.7988600 0.1991111 -0.8678454 -1.1328696</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 1.4020096 0.1991111 -0.2018550 0.8005604</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] 27 42 47 19 21 32 7 27 11 32</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 47 47 48 11 25 47 41 41 25 43</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] 0.03968726 1.23030512 1.62717774 -0.59530893 -0.43655988 0.43655988</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -1.54780321 0.03968726 -1.23030512 0.43655988</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.7483177 0.7483177 0.8270879 -2.0874124 -0.9846285 0.7483177</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.2756960 0.2756960 -0.9846285 0.4332365</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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@ -231,35 +230,35 @@
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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 2 >=16</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B I 31 4 >=16</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C S 22 4 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D R 18 1 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E I 18 0.5 >=16</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F S 25 1 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G I 30 2 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H I 25 0.5 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I R 31 2 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J I 19 4 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A I 23 2 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B R 24 2 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C I 17 4 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D I 28 >=8 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E R 21 2 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F I 22 0.25 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G S 28 >=8 <=1</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H R 22 1 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I R 24 4 <=1</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J I 30 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" 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] 0.2382463 0.7955297 -0.1157524 -0.2672839 -0.4858364 -0.4005406</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.4131124 -0.4981535 0.5828624 -0.2621839</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.36533824 0.18335833 -0.58549269 0.60903763 -0.01036260 -0.61484124</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.02482806 0.20385648 0.03371288 0.57089751</span>
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<span class="r-in"><span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span> <span class="op"><-</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span>, <span class="fu">where</span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span><span class="op">)</span></span></span>
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<span class="r-msg co"><span class="r-pr">#></span> ℹ Calculating mean AMR distance based on columns "gent" and "tobr"</span>
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<span class="r-in"><span><span class="va">y</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/order.html" class="external-link">order</a></span><span class="op">(</span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span><span class="op">)</span>, <span class="op">]</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr amr_distance</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D R 18 1 0.5 -0.8682389</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H I 25 0.5 2 -0.8274710</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F S 25 1 1 -0.6322451</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I R 31 2 0.5 -0.4370192</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E I 18 0.5 >=16 -0.1194896</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C S 22 4 1 0.2301943</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J I 19 4 1 0.2301943</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G I 30 2 8 0.5069560</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A S 24 2 >=16 0.7429498</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B I 31 4 >=16 1.1741694</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F I 22 0.25 4 -0.59700430</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I R 24 4 <=1 -0.52643647</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A I 23 2 2 -0.22714558</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B R 24 2 2 -0.22714558</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E R 21 2 2 -0.22714558</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G S 28 >=8 <=1 -0.19186166</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H R 22 1 4 0.07214531</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C I 17 4 2 0.10742922</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J I 30 4 4 0.74129491</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D I 28 >=8 4 1.07586972</span>
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<span class="r-in"><span></span></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="va">y</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
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@ -272,16 +271,16 @@
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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 4 1 -0.1157524 0.0000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 J I 19 4 1 -0.2621839 0.1464315</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 D R 18 1 0.5 -0.2672839 0.1515315</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 F S 25 1 1 -0.4005406 0.2847882</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 A S 24 2 >=16 0.2382463 0.3539987</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 E I 18 0.5 >=16 -0.4858364 0.3700839</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 H I 25 0.5 2 -0.4981535 0.3824011</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 G I 30 2 8 0.4131124 0.5288649</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I R 31 2 0.5 0.5828624 0.6986148</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 B I 31 4 >=16 0.7955297 0.9112821</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 C I 17 4 2 -0.58549269 0.00000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 F I 22 0.25 4 -0.61484124 0.02934854</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 A I 23 2 2 -0.36533824 0.22015446</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 G S 28 >=8 <=1 -0.02482806 0.56066463</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E R 21 2 2 -0.01036260 0.57513009</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 I R 24 4 <=1 0.03371288 0.61920557</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 B R 24 2 2 0.18335833 0.76885102</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H R 22 1 4 0.20385648 0.78934918</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 J I 30 4 4 0.57089751 1.15639020</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 D I 28 >=8 4 0.60903763 1.19453032</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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