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Built site for AMR: 1.8.2.9088@08fe5a8
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="">1.8.2.9086</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9088</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] S R R R I I I R S R</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] S I S R S I S S S S</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] -0.9486833 0.9486833 0.9486833 0.9486833 -0.9486833 -0.9486833</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.9486833 0.9486833 -0.9486833 0.9486833</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-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 0.025 >=128 0.025 >=128 16 4 >=128 8 0.025</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.005 32 >=64 0.001 32 0.005 >=64 0.001 >=64 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] -0.09761619 -1.32347254 1.06581655 -1.32347254 1.06581655 0.48410018</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.09628927 1.06581655 0.29019472 -1.32347254</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.9977554 0.7020018 0.8364352 -1.3099002 0.7020018 -0.9977554</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.8364352 -1.3099002 0.8364352 0.7020018</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] -0.09761619 -1.32347254 1.06581655 -1.32347254 1.06581655 0.48410018</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.09628927 1.06581655 0.29019472 -1.32347254</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.9977554 0.7020018 0.8364352 -1.3099002 0.7020018 -0.9977554</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.8364352 -1.3099002 0.8364352 0.7020018</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] 44 29 31 8 26 23 36 34 41 46</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 43 13 6 50 43 19 14 23 8 44</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] 1.0822909 -0.2483946 -0.0709699 -2.1113544 -0.5145317 -0.7806689</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.3725920 0.1951672 0.8161538 1.2597157</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.9878564 -0.7867359 -1.2008074 1.4019279 0.9878564 -0.4318175</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.7275828 -0.1952051 -1.0825013 1.0470094</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 27 0.5 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B I 27 2 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C S 20 >=8 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D I 27 4 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E I 22 4 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F S 31 2 <=1</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G S 26 1 >=16</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H R 21 4 <=1</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I R 31 4 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J S 30 4 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A I 22 4 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B I 24 0.5 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C R 30 2 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D S 29 0.5 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E I 30 4 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F R 19 0.25 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G I 26 4 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H S 22 2 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I S 29 2 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J I 28 0.5 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" 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] -0.50096961 -0.27264058 0.11352599 -0.05965490 -0.17279077 -0.22166036</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.04514514 -0.03730406 0.78189474 0.32445439</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.03769893 -0.40858317 0.58133901 -0.40733070 0.47139759 0.01703862</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.53378217 -0.20375172 -0.07522511 -0.47096776</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> 1 A I 27 0.5 4 -0.8642174</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F S 31 2 <=1 -0.8028441</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B I 27 2 2 -0.4075594</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H R 21 4 <=1 -0.3768727</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D I 27 4 2 0.0184120</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I R 31 4 2 0.0184120</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G S 26 1 >=16 0.3523234</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E I 22 4 4 0.4136967</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J S 30 4 4 0.4136967</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C S 20 >=8 8 1.2349528</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D S 29 0.5 1 -0.97204037</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J I 28 0.5 1 -0.97204037</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B I 24 0.5 2 -0.33817468</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C R 30 2 1 -0.30782920</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I S 29 2 1 -0.30782920</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F R 19 0.25 4 -0.03641457</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H S 22 2 2 0.32603649</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A I 22 4 2 0.65814207</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E I 30 4 2 0.65814207</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G I 26 4 4 1.29200776</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 S 20 >=8 8 0.11352599 0.00000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 G S 26 1 >=16 0.04514514 0.06838084</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 H R 21 4 <=1 -0.03730406 0.15083004</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D I 27 4 2 -0.05965490 0.17318088</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 J S 30 4 4 0.32445439 0.21092841</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 E I 22 4 4 -0.17279077 0.28631675</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 F S 31 2 <=1 -0.22166036 0.33518634</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 B I 27 2 2 -0.27264058 0.38616657</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 A I 27 0.5 4 -0.50096961 0.61449559</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 I R 31 4 2 0.78189474 0.66836876</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 C R 30 2 1 0.58133901 0.00000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 G I 26 4 4 0.53378217 0.04755684</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 E I 30 4 2 0.47139759 0.10994142</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 F R 19 0.25 4 0.01703862 0.56430040</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 A I 22 4 2 -0.03769893 0.61903794</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 I S 29 2 1 -0.07522511 0.65656413</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 H S 22 2 2 -0.20375172 0.78509073</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 D S 29 0.5 1 -0.40733070 0.98866971</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 B I 24 0.5 2 -0.40858317 0.98992219</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J I 28 0.5 1 -0.47096776 1.05230677</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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