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https://github.com/msberends/AMR.git
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Built site for AMR: 2.0.0.9011@2758615
This commit is contained in:
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@ -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="">2.0.0.9009</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9011</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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@ -201,30 +201,31 @@
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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 R R I S R R R R S</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] I I R S R S R R R 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 -1.449138 -1.449138 0.621059 0.621059</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-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-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] 64 0.125 32 4 0.0625 0.001 4 128 4 64 </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 4 >=32 0.005 8 <=0.001 0.025 >=32 2 0.0625 </span>
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<span class="r-out co"><span class="r-pr">#></span> [10] 0.025 </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] 0.8649908 -0.7925812 0.6808161 0.1282921 -0.9767559 -2.0755022</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.1282921 1.0491654 0.1282921 0.8649908</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.6643931 1.2141827 -1.1029707 0.8476563 -1.5284946 -0.6774467</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 1.2141827 0.4811299 -0.4351860 -0.6774467</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] 0.8649908 -0.7925812 0.6808161 0.1282921 -0.9767559 -2.0755022</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.1282921 1.0491654 0.1282921 0.8649908</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.6643931 1.2141827 -1.1029707 0.8476563 -1.5284946 -0.6774467</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 1.2141827 0.4811299 -0.4351860 -0.6774467</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] 8 50 16 42 22 38 39 29 34 28</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 37 30 32 24 18 32 47 10 37 15</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] -1.7802697 1.5281961 -1.1500857 0.8980121 -0.6774478 0.5829202</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.6616932 -0.1260368 0.2678282 -0.2048098</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.7726039 0.1580326 0.3336244 -0.3687428 -0.8955181 0.3336244</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 1.6505628 -1.5978853 0.7726039 -1.1589058</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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@ -234,22 +235,22 @@
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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 4 <=2</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B S 17 2 <=2</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C R 31 <=0.25 16</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D R 18 0.5 <=2</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E I 19 <=0.25 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F I 30 0.5 16</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G R 20 1 <=2</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H I 31 <=0.25 <=2</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I I 27 2 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J S 19 4 8</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 18 4 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 I 23 <=0.5 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D R 28 <=0.5 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E S 21 <=0.5 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F S 25 4 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G I 28 1 <=0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H S 23 4 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I I 29 >=8 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J S 24 >=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",</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] -0.06541043 -0.48291290 0.75508761 -0.23028094 -0.47858500 0.34807060</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.01180992 -0.33212745 0.33539338 0.13895522</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.38190897 -0.59575522 -0.53742256 0.55691259 -0.19601880 0.04336306</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.31201874 0.38476682 0.90237881 0.13570302</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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@ -265,17 +266,17 @@
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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 31 <=0.25 16 0.75508761 0.0000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 F I 30 0.5 16 0.34807060 0.4070170</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 I I 27 2 8 0.33539338 0.4196942</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 J S 19 4 8 0.13895522 0.6161324</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 G R 20 1 <=2 0.01180992 0.7432777</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 A S 23 4 <=2 -0.06541043 0.8204980</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 D R 18 0.5 <=2 -0.23028094 0.9853685</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H I 31 <=0.25 <=2 -0.33212745 1.0872151</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 E I 19 <=0.25 8 -0.47858500 1.2336726</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 B S 17 2 <=2 -0.48291290 1.2380005</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 I 23 <=0.5 1 -0.53742256 0.00000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B S 17 2 1 -0.59575522 0.05833266</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 A I 18 4 1 -0.38190897 0.15551359</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 G I 28 1 <=0.5 -0.31201874 0.22540382</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E S 21 <=0.5 4 -0.19601880 0.34140376</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F S 25 4 1 0.04336306 0.58078562</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 J S 24 >=8 1 0.13570302 0.67312558</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H S 23 4 4 0.38476682 0.92218938</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 D R 28 <=0.5 1 0.55691259 1.09433515</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 I I 29 >=8 4 0.90237881 1.43980137</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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