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https://github.com/msberends/AMR.git
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Built site for AMR: 2.0.0.9006@ed70f95
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="">2.0.0.9005</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9006</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] R I S S I R S I R R</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] R R R S R I 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] 1.1618950 -0.7745967 -0.7745967 -0.7745967 -0.7745967 1.1618950</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.7745967 -0.7745967 1.1618950 1.1618950</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 1.1618950 1.1618950 1.1618950 -0.7745967 1.1618950 -0.7745967</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.7745967 -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] 0.025 0.01 128 32 0.025 <=0.002 <=0.002 8 64 </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] 0.125 4 16 >=256 0.002 0.01 0.0625 2 >=256 128 </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] -0.6668789 -0.8627824 1.1591730 0.8627824 -0.6668789 -1.2068812</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -1.2068812 0.5663918 1.0109777 1.0109777</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.60649465 0.20453613 0.52894844 1.17777307 -1.57418159 -1.19755056</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.76870081 0.04232998 1.17777307 1.01556691</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] -0.6668789 -0.8627824 1.1591730 0.8627824 -0.6668789 -1.2068812</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -1.2068812 0.5663918 1.0109777 1.0109777</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.60649465 0.20453613 0.52894844 1.17777307 -1.57418159 -1.19755056</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.76870081 0.04232998 1.17777307 1.01556691</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] 6 6 47 20 16 48 50 42 40 30</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 39 30 35 42 40 19 36 39 47 33</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] -1.41385375 -1.41385375 0.95218722 -0.60593732 -0.83677059 1.00989554</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 1.12531217 0.66364564 0.54822900 -0.02885416</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.3924186 -0.7848373 -0.1308062 0.7848373 0.5232249 -2.2237057</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.0000000 0.3924186 1.4388684 -0.3924186</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 27 <=0.5 16</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B I 24 <=0.5 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C R 21 >=16 16</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D I 18 <=0.5 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E I 27 8 16</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F S 28 >=16 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G R 28 4 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H I 20 <=0.5 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I S 19 <=0.5 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J S 29 >=16 16</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 30 1 <=0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B S 23 1 16</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C I 17 8 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D R 20 >=16 16</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E S 25 <=0.5 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F S 19 1 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G I 27 <=0.5 <=0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H R 26 8 16</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I R 18 2 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J R 20 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] 0.06722963 -0.51689491 0.82743999 -0.87165479 0.48486417 0.44502714</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.42239233 -0.95677380 -0.60915584 0.70752609</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.2236361 -0.0243641 -0.3696267 0.8211210 -0.5440220 -0.4545619</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.5293690 1.0323298 0.1055421 0.1865871</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 21 >=16 16 0.82743999 0.0000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 J S 29 >=16 16 0.70752609 0.1199139</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 E I 27 8 16 0.48486417 0.3425758</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 F S 28 >=16 8 0.44502714 0.3824128</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 G R 28 4 2 0.42239233 0.4050477</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 A S 27 <=0.5 16 0.06722963 0.7602104</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 B I 24 <=0.5 4 -0.51689491 1.3443349</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 I S 19 <=0.5 8 -0.60915584 1.4365958</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 D I 18 <=0.5 4 -0.87165479 1.6990948</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 H I 20 <=0.5 2 -0.95677380 1.7842138</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 17 8 1 -0.3696267 0.00000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 F S 19 1 4 -0.4545619 0.08493517</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 A I 30 1 <=0.25 -0.2236361 0.14599062</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 G I 27 <=0.5 <=0.25 -0.5293690 0.15974230</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E S 25 <=0.5 0.5 -0.5440220 0.17439527</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 B S 23 1 16 -0.0243641 0.34526264</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 I R 18 2 4 0.1055421 0.47516879</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 J R 20 8 0.5 0.1865871 0.55621386</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 D R 20 >=16 16 0.8211210 1.19074770</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 H R 26 8 16 1.0323298 1.40195650</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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