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Built site for AMR: 2.0.0.9007@1a02d30
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="">2.0.0.9006</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9007</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 S R I S I I S</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] I R S S S R R I R I</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 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-out co"><span class="r-pr">#></span> [1] -0.7745967 1.1618950 -0.7745967 -0.7745967 -0.7745967 1.1618950</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 1.1618950 -0.7745967 1.1618950 -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] 0.125 4 16 >=256 0.002 0.01 0.0625 2 >=256 128 </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] <=0.001 0.025 32 0.01 0.0625 0.125 0.5 0.01 8 </span>
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<span class="r-out co"><span class="r-pr">#></span> [10] 2 </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] -0.60649465 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-out co"><span class="r-pr">#></span> [1] -1.5257422 -0.5427941 1.6420106 -0.8226018 -0.2629864 -0.0513201</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.3720126 -0.8226018 1.2186779 0.7953453</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] -0.60649465 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-out co"><span class="r-pr">#></span> [1] -1.5257422 -0.5427941 1.6420106 -0.8226018 -0.2629864 -0.0513201</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.3720126 -0.8226018 1.2186779 0.7953453</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] 39 30 35 42 40 19 36 39 47 33</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 16 44 41 26 44 46 48 50 48 40</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] 0.3924186 -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-out co"><span class="r-pr">#></span> [1] -2.23059935 0.33963858 0.06425595 -1.31265723 0.33963858 0.52322701</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.70681543 0.89040385 0.70681543 -0.02753826</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 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-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 21 >=4 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B R 28 2 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C S 23 >=4 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D I 20 1 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E I 27 1 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F S 20 2 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G I 25 >=4 <=0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H S 25 2 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I R 20 1 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J R 22 >=4 <=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] -0.2236361 -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-out co"><span class="r-pr">#></span> [1] 0.37458457 0.92678423 0.01430793 -0.80688677 -0.22319302 -0.25784351</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.08244556 0.15908059 -0.28933760 0.18494914</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 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-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 23 >=4 1 0.01430793 0.0000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 G I 25 >=4 <=0.5 -0.08244556 0.0967535</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 H S 25 2 2 0.15908059 0.1447727</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 J R 22 >=4 <=0.5 0.18494914 0.1706412</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E I 27 1 1 -0.22319302 0.2375010</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F S 20 2 2 -0.25784351 0.2721514</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 I R 20 1 1 -0.28933760 0.3036455</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 A I 21 >=4 4 0.37458457 0.3602766</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 D I 20 1 1 -0.80688677 0.8211947</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 B R 28 2 2 0.92678423 0.9124763</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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