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https://github.com/msberends/AMR.git
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Built site for AMR: 1.8.2.9146@1d3d7d4
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="">1.8.2.9145</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9146</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] S S I I R I I R I R</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] S R I S S R S I I 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">sir</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.621059 -0.621059 -0.621059 -0.621059 1.449138 -0.621059 -0.621059</span>
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<span class="r-out co"><span class="r-pr">#></span> [8] 1.449138 -0.621059 1.449138</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 1.8973666</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-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] 0.01 0.5 0.0625 <=0.001 >=128 0.5 32 >=128 0.002 </span>
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<span class="r-out co"><span class="r-pr">#></span> [10] 64 </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.25 64 64 0.01 0.025 128 256 4 128 256 </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] -0.90187954 -0.05159359 -0.50356433 -1.40235097 1.15366171 -0.05159359</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.85234788 1.15366171 -1.25169406 1.00300479</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.8840919 0.5294878 0.5294878 -1.7046495 -1.4710682 0.7061853</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.8828827 -0.1773020 0.7061853 0.8828827</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] -0.90187954 -0.05159359 -0.50356433 -1.40235097 1.15366171 -0.05159359</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.85234788 1.15366171 -1.25169406 1.00300479</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.8840919 0.5294878 0.5294878 -1.7046495 -1.4710682 0.7061853</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.8828827 -0.1773020 0.7061853 0.8828827</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] 31 43 47 11 50 40 41 6 40 11</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 13 36 18 50 14 40 38 15 45 48</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] -0.06075813 0.66833944 0.91137196 -1.27592075 1.09364635 0.48606505</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.54682318 -1.57971140 0.48606505 -1.27592075</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -1.2438749 0.2860247 -0.9112880 1.2172680 -1.1773575 0.5520942</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.4190595 -1.1108402 0.8846811 1.0842332</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 S 23 <=0.25 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B S 22 <=0.25 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C R 22 2 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D S 29 2 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E R 25 >=4 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F I 17 0.5 >=4</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G R 29 >=4 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H R 19 0.5 >=4</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I R 24 1 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J I 22 0.5 2</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 17 <=1 <=0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B R 20 <=1 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C R 28 >=16 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D R 22 >=16 <=0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E I 24 >=16 >=4</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F R 30 >=16 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G R 17 >=16 >=4</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H I 23 2 >=4</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I I 27 8 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J R 19 8 0.5</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",</span>
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<span class="r-msg co"><span class="r-pr">#></span> and "tobr"</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.6549761 -0.4877892 0.2461508 0.2294569 0.3737749 -0.4180608</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.8678531 0.1870373 -0.0197123 -0.3237347</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -1.29633203 -0.33470083 0.68999803 0.04843526 0.30058957 0.64264079</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.40191868 -0.19451042 -0.15234167 -0.10569739</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",</span>
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<span class="r-msg co"><span class="r-pr">#></span> and "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 22 2 1 0.2461508 0.00000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 D S 29 2 1 0.2294569 0.01669387</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 H R 19 0.5 >=4 0.1870373 0.05911349</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 E R 25 >=4 0.5 0.3737749 0.12762412</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 I R 24 1 0.5 -0.0197123 0.26586311</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 J I 22 0.5 2 -0.3237347 0.56988550</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G R 29 >=4 1 0.8678531 0.62170227</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 F I 17 0.5 >=4 -0.4180608 0.66421164</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 B S 22 <=0.25 2 -0.4877892 0.73393999</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 A S 23 <=0.25 1 -0.6549761 0.90112686</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 28 >=16 1 0.68999803 0.00000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 F R 30 >=16 0.5 0.64264079 0.04735723</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 G R 17 >=16 >=4 0.40191868 0.28807934</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 E I 24 >=16 >=4 0.30058957 0.38940845</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 D R 22 >=16 <=0.25 0.04843526 0.64156276</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 J R 19 8 0.5 -0.10569739 0.79569542</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 I I 27 8 0.5 -0.15234167 0.84233970</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H I 23 2 >=4 -0.19451042 0.88450845</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 B R 20 <=1 1 -0.33470083 1.02469886</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 A I 17 <=1 <=0.25 -1.29633203 1.98633005</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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