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Built site for AMR: 1.8.2.9098@19fd0ef
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="">1.8.2.9096</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9098</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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@ -191,31 +191,31 @@
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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 I S S S S S I S R</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] S I S R R R S R R 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] 1.8973666 -0.4743416 -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 -0.4743416 -0.4743416 1.8973666</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -1.1618950 -1.1618950 -1.1618950 0.7745967 0.7745967 0.7745967</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -1.1618950 0.7745967 0.7745967 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] 0.005 <=0.002 0.005 0.005 <=0.002 2 64 256 0.025 </span>
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<span class="r-out co"><span class="r-pr">#></span> [10] 16 </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.125 0.0625 0.25 64 0.0625 32 <=0.001 0.01 8 </span>
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<span class="r-out co"><span class="r-pr">#></span> [10] >=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] -0.7319933 -0.9284550 -0.7319933 -0.7319933 -0.9284550 0.5526353</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 1.2957230 1.5929580 -0.3869141 0.9984879</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.3704641 -0.5436561 -0.1972720 1.1882645 -0.5436561 1.0150725</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -1.5768826 -1.0015510 0.6686883 1.3614566</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] -0.7319933 -0.9284550 -0.7319933 -0.7319933 -0.9284550 0.5526353</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 1.2957230 1.5929580 -0.3869141 0.9984879</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.3704641 -0.5436561 -0.1972720 1.1882645 -0.5436561 1.0150725</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -1.5768826 -1.0015510 0.6686883 1.3614566</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] 43 18 9 46 21 44 15 7 12 40</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 37 48 42 45 41 36 45 11 9 26</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] 1.1037355 -0.4730295 -1.0406649 1.2929473 -0.2838177 1.1668061</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.6622413 -1.1668061 -0.8514531 0.9145237</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.2132007 0.9949367 0.5685352 0.7817360 0.4974683 0.1421338</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.7817360 -1.6345388 -1.7766726 -0.5685352</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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@ -226,35 +226,35 @@
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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 R 19 <=1 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B S 19 >=4 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C S 19 2 0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D I 27 >=4 >=8</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E R 24 <=1 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F S 30 2 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G I 31 <=1 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H I 18 2 0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I I 27 <=1 0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J S 22 2 >=8</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A S 26 >=8 <=1</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B S 17 2 <=1</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C S 22 4 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D I 21 4 <=1</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E S 18 >=8 <=1</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F R 26 <=1 <=1</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G S 17 2 <=1</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H I 31 <=1 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I R 21 2 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J R 20 >=8 <=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] 0.10395052 0.01413264 -0.56431322 0.81427297 0.35886977 0.25802215</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.13868335 -0.61529708 -0.47337526 0.24242087</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.21379008 -0.70858534 0.29772954 -0.27497563 -0.22745796 0.09238219</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.70858534 0.36816222 0.54713702 0.40040322</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> 9 I I 27 <=1 0.25 -1.0562699</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G I 31 <=1 0.5 -0.7947569</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C S 19 2 0.25 -0.4224042</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H I 18 2 0.25 -0.4224042</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A R 19 <=1 2 -0.2717308</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E R 24 <=1 2 -0.2717308</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F S 30 2 1 0.1006218</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B S 19 >=4 1 0.7344875</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J S 22 2 >=8 0.8851609</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D I 27 >=4 >=8 1.5190266</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F R 26 <=1 <=1 -0.99208370</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B S 17 2 <=1 -0.56611233</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G S 17 2 <=1 -0.56611233</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D I 21 4 <=1 -0.14014095</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H I 31 <=1 4 0.04301464</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A S 26 >=8 <=1 0.28583042</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E S 18 >=8 <=1 0.28583042</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J R 20 >=8 <=1 0.28583042</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I R 21 2 4 0.46898601</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C S 22 4 4 0.89495739</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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@ -267,16 +267,16 @@
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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 19 2 0.25 -0.56431322 0.00000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 H I 18 2 0.25 -0.61529708 0.05098385</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 I I 27 <=1 0.25 -0.47337526 0.09093796</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 G I 31 <=1 0.5 -0.13868335 0.42562987</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 B S 19 >=4 1 0.01413264 0.57844586</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 A R 19 <=1 2 0.10395052 0.66826374</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 J S 22 2 >=8 0.24242087 0.80673409</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 F S 30 2 1 0.25802215 0.82233538</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 E R 24 <=1 2 0.35886977 0.92318299</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 D I 27 >=4 >=8 0.81427297 1.37858619</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 C S 22 4 4 0.29772954 0.00000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 H I 31 <=1 4 0.36816222 0.07043268</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 A S 26 >=8 <=1 0.21379008 0.08393946</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 J R 20 >=8 <=1 0.40040322 0.10267368</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 F R 26 <=1 <=1 0.09238219 0.20534735</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> 6 I R 21 2 4 0.54713702 0.24940748</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> 7 E S 18 >=8 <=1 -0.22745796 0.52518750</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> 8 D I 21 4 <=1 -0.27497563 0.57270518</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> 9 B S 17 2 <=1 -0.70858534 1.00631489</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> 10 G S 17 2 <=1 -0.70858534 1.00631489</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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Reference in New Issue
Block a user