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Built site for AMR@2.1.1.9140: baea432
This commit is contained in:
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@ -7,7 +7,7 @@
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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="">2.1.1.9139</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9140</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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@ -109,31 +109,30 @@
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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 S R S R S R</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] S S I I I S S S 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] -0.621059 -0.621059 -0.621059 -0.621059 -0.621059 1.449138 -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 -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 1.8973666 1.8973666</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 <=0.002 >=128 64 0.01 0.0625 0.125 8 </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-out co"><span class="r-pr">#></span> [1] 0.025 1 0.001 8 0.5 16 64 128 4 64 </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] -0.79195592 -1.01052933 -1.01052933 1.62932373 1.46397933 -0.62661152</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.18946469 -0.02412029 0.96794612 -0.40803811</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -1.1967905 -0.2158758 -2.0527259 0.3370712 -0.4001915 0.5213868</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.8900182 1.0743338 0.1527555 0.8900182</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] -0.79195592 -1.01052933 -1.01052933 1.62932373 1.46397933 -0.62661152</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.18946469 -0.02412029 0.96794612 -0.40803811</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -1.1967905 -0.2158758 -2.0527259 0.3370712 -0.4001915 0.5213868</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.8900182 1.0743338 0.1527555 0.8900182</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] 37 13 9 50 9 10 12 46 11 49</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 42 8 24 15 32 45 46 42 49 14</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] 0.6757607 -0.6321633 -0.8501506 1.3842196 -0.8501506 -0.7956538</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.6866601 1.1662323 -0.7411569 1.3297228</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.67331608 -1.54928069 -0.50335280 -1.09168723 0.01961115 0.86942756</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.93479805 0.67331608 1.13090953 -1.15705773</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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@ -143,22 +142,22 @@
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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 I 26 >=8 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B R 19 4 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C R 26 >=8 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D S 23 4 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E R 30 >=8 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F R 24 1 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G R 25 >=8 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H S 25 <=0.5 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I S 17 2 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J S 19 2 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 R 27 8 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B I 21 8 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C S 22 2 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D R 22 4 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E S 19 8 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F S 30 2 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G R 20 16 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H R 27 4 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I S 20 1 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J R 17 16 4</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> <span style="color: #0000BB;">ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",</span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;"> and "tobr"</span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.28451298 -0.01875836 0.27473171 0.08104917 0.68750659 -0.05708302</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.85737880 -0.96761082 -0.47233937 -0.66938769</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.27346725 0.04720942 -0.67302993 0.39497313 -0.68358519 0.01305317</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.64812902 0.49329507 -0.98062442 0.46711247</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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@ -174,17 +173,17 @@
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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> <span style="color: #0000BB;">ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",</span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;"> and "tobr"</span></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 26 >=8 0.5 0.27473171 0.000000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 A I 26 >=8 4 0.28451298 0.009781269</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 D S 23 4 8 0.08104917 0.193682539</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 B R 19 4 2 -0.01875836 0.293490073</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 F R 24 1 2 -0.05708302 0.331814730</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 E R 30 >=8 1 0.68750659 0.412774877</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G R 25 >=8 8 0.85737880 0.582647082</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 I S 17 2 8 -0.47233937 0.747071081</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 J S 19 2 2 -0.66938769 0.944119407</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 H S 25 <=0.5 0.5 -0.96761082 1.242342534</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 22 2 1 -0.67302993 0.00000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 E S 19 8 0.5 -0.68358519 0.01055526</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 I S 20 1 1 -0.98062442 0.30759449</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 F S 30 2 2 0.01305317 0.68608310</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 B I 21 8 4 0.04720942 0.72023935</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 A R 27 8 0.5 0.27346725 0.94649718</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 D R 22 4 4 0.39497313 1.06800305</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 J R 17 16 4 0.46711247 1.14014240</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 H R 27 4 2 0.49329507 1.16632499</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 G R 20 16 4 0.64812902 1.32115894</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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