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Built site for AMR: 1.8.2.9151@9179e98
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="">1.8.2.9150</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9151</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 I S R I I S I R I</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] I R S S I I R S 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] -0.4743416 -0.4743416 -0.4743416 1.8973666 -0.4743416 -0.4743416</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.4743416 -0.4743416 1.8973666 -0.4743416</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.621059 1.449138 -0.621059 -0.621059 -0.621059 -0.621059 1.449138</span>
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<span class="r-out co"><span class="r-pr">#></span> [8] -0.621059 1.449138 -0.621059</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] 0.0625 <=0.001 0.0625 128 0.0625 64 256 8 0.0625 </span>
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<span class="r-out co"><span class="r-pr">#></span> [10] 0.002 </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.125 64 0.0625 1 <=0.01 2 0.025 2 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">mic</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.4417215 -1.3482772 -0.4417215 1.2298295 -0.4417215 1.0778703</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 1.3817887 0.6219928 -0.4417215 -1.1963180</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.53828759 1.76490658 -0.79419805 0.22944380 -1.47078851 0.48535426</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -1.13249328 0.48535426 0.99717519 -0.02646666</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] -0.4417215 -1.3482772 -0.4417215 1.2298295 -0.4417215 1.0778703</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 1.3817887 0.6219928 -0.4417215 -1.1963180</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.53828759 1.76490658 -0.79419805 0.22944380 -1.47078851 0.48535426</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -1.13249328 0.48535426 0.99717519 -0.02646666</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 43 46 31 33 33 37 43 45 27</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 43 46 34 46 35 11 29 42 49 42</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] -2.3345712 0.7372330 1.0005305 -0.3159570 -0.1404253 -0.1404253</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.2106380 0.7372330 0.9127647 -0.6670203</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.4708967 0.7374420 -0.3287392 0.7374420 -0.2398908 -2.3722532</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.7729814 0.3820483 1.0039873 0.3820483</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 R 29 >=8 <=0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B S 31 1 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C S 27 >=8 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D R 25 2 <=0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E R 27 0.5 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F I 22 0.5 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G R 22 0.5 16</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H I 23 4 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I S 27 0.5 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J R 20 4 4</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 29 0.5 >=4</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B R 23 4 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C R 19 0.5 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D S 23 0.5 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E I 29 2 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F I 23 1 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G I 18 4 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H S 19 1 >=4</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I S 26 8 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J S 20 4 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] 0.487327335 0.218326088 0.247132119 -0.092191622 0.008553263</span>
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<span class="r-out co"><span class="r-pr">#></span> [6] -0.823174446 0.153968346 0.065818788 -0.465788386 0.200028515</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.8356833 0.6493326 -0.4169825 -0.6870116 0.3357761 -0.5197242</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.1776166 -0.1333786 0.4847109 -0.3707894</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 S 27 >=8 2 0.247132119 0.00000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B S 31 1 4 0.218326088 0.02880603</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 J R 20 4 4 0.200028515 0.04710360</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 G R 22 0.5 16 0.153968346 0.09316377</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 H I 23 4 8 0.065818788 0.18131333</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 E R 27 0.5 1 0.008553263 0.23857886</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 A R 29 >=8 <=0.25 0.487327335 0.24019522</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 D R 25 2 <=0.25 -0.092191622 0.33932374</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I S 27 0.5 1 -0.465788386 0.71292051</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 F I 22 0.5 1 -0.823174446 1.07030656</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 0.5 1 -0.4169825 0.00000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 J S 20 4 1 -0.3707894 0.04619304</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 F I 23 1 1 -0.5197242 0.10274173</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 G I 18 4 2 -0.1776166 0.23936587</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 D S 23 0.5 1 -0.6870116 0.27002914</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 H S 19 1 >=4 -0.1333786 0.28360392</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 E I 29 2 2 0.3357761 0.75275856</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 I S 26 8 2 0.4847109 0.90169334</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 B R 23 4 2 0.6493326 1.06631508</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 A R 29 0.5 >=4 0.8356833 1.25266578</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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