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Built site for AMR: 1.8.2.9094@593d740
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="">1.8.2.9093</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9094</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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@ -191,30 +191,30 @@
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<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">rsi</span> <span class="op"><-</span> <span class="fu"><a href="random.html">random_rsi</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">rsi</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> Class 'rsi'</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] I I I R S I I I I I</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] S S I R S I R S 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">rsi</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.3162278 -0.3162278 -0.3162278 2.8460499 -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-out co"><span class="r-pr">#></span> [1] -0.621059 -0.621059 -0.621059 1.449138 -0.621059 -0.621059 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-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] 4 >=64 0.001 1 0.0625 0.0625 0.25 0.0625 4 4 </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.125 2 8 0.5 0.002 4 0.025 4 32 128 </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] 0.7050535 1.5873138 -1.9341805 0.2639234 -0.6183369 -0.6183369</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.1772067 -0.6183369 0.7050535 0.7050535</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.6558590 0.1714027 0.5850335 -0.2422282 -1.8896751 0.3782181</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -1.1360695 0.3782181 0.9986643 1.4122951</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] 0.7050535 1.5873138 -1.9341805 0.2639234 -0.6183369 -0.6183369</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.1772067 -0.6183369 0.7050535 0.7050535</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.6558590 0.1714027 0.5850335 -0.2422282 -1.8896751 0.3782181</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -1.1360695 0.3782181 0.9986643 1.4122951</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 50 21 40 26 10 16 45 24 19</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 47 10 18 45 33 35 18 41 45 47</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] 0.6768341 1.5693625 -0.5875812 0.8255888 -0.2156944 -1.4057323</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.9594681 1.1974757 -0.3644491 -0.7363360</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.94791030 -1.72939361 -1.15051709 0.80319117 -0.06512361 0.07959552</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -1.15051709 0.51375291 0.80319117 0.94791030</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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@ -225,35 +225,35 @@
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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 I 30 8 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B S 17 4 >=4</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C R 19 8 >=4</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D R 29 2 >=4</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E I 19 8 <=1</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F R 28 8 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G R 26 8 >=4</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H I 25 1 >=4</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I R 27 4 >=4</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J R 21 0.5 <=1</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A S 17 0.25 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B I 31 1 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C I 24 >=4 16</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D S 24 0.25 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E R 31 >=4 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F S 19 0.5 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G S 27 0.5 16</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H I 31 0.5 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I R 18 0.25 0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J R 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] 0.09446764 -0.47291812 0.29008010 0.47684186 -0.78696988 0.47223165</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.66233628 -0.39251526 0.54299934 -0.88655361</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.89400136 0.13637933 0.51178793 -0.33268016 0.81891467 -0.78894215</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.20168990 -0.01042573 -0.59026102 0.94753861</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> 10 J R 21 0.5 <=1 -1.83069295</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E I 19 8 <=1 -0.45056183</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H I 25 1 >=4 -0.29980604</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D R 29 2 >=4 0.04522674</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A I 30 8 2 0.14236523</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F R 28 8 2 0.14236523</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B S 17 4 >=4 0.39025951</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I R 27 4 >=4 0.39025951</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C R 19 8 >=4 0.73529229</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G R 26 8 >=4 0.73529229</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I R 18 0.25 0.25 -1.27088082</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A S 17 0.25 1 -0.75638506</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F S 19 0.5 0.5 -0.72002283</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D S 24 0.25 4 -0.24188931</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H I 31 0.5 2 -0.20552708</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B I 31 1 2 0.08808303</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E R 31 >=4 1 0.41805537</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G S 27 0.5 16 0.56621656</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J R 31 >=4 2 0.67530325</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C I 24 >=4 16 1.44704689</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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@ -266,16 +266,16 @@
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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 R 19 8 >=4 0.29008010 0.0000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 F R 28 8 2 0.47223165 0.1821516</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 D R 29 2 >=4 0.47684186 0.1867618</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 A I 30 8 2 0.09446764 0.1956125</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 I R 27 4 >=4 0.54299934 0.2529192</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 G R 26 8 >=4 0.66233628 0.3722562</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 H I 25 1 >=4 -0.39251526 0.6825954</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 B S 17 4 >=4 -0.47291812 0.7629982</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 E I 19 8 <=1 -0.78696988 1.0770500</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J R 21 0.5 <=1 -0.88655361 1.1766337</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 C I 24 >=4 16 0.51178793 0.0000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 E R 31 >=4 1 0.81891467 0.3071267</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 G S 27 0.5 16 0.20168990 0.3100980</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 B I 31 1 2 0.13637933 0.3754086</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 J R 31 >=4 2 0.94753861 0.4357507</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 H I 31 0.5 2 -0.01042573 0.5222137</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 D S 24 0.25 4 -0.33268016 0.8444681</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 I R 18 0.25 0.25 -0.59026102 1.1020490</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 F S 19 0.5 0.5 -0.78894215 1.3007301</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 A S 17 0.25 1 -0.89400136 1.4057893</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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