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Built site for AMR@2.1.1.9217: 4dc4398
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="">2.1.1.9216</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9217</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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@@ -111,30 +111,31 @@
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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] S R I I S R S S S R</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] S S I I I R R S 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] -0.621059 1.449138 -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] -0.621059 -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 1.8973666</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 1.8973666 -0.4743416 -0.4743416 -0.4743416</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 0.25 1 2 >=16 8 1 1 0.025 4 </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] >=128 0.125 0.01 64 64 8 0.002 1 >=128 </span>
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<span class="r-out co"><span class="r-pr">#></span> [10] <=0.001</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] -1.9714967 -0.4147020 0.1369756 0.4128144 1.2403309 0.9644921</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.1369756 0.1369756 -1.3310188 0.6886533</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 1.02853908 -0.44976893 -0.98844311 0.88070828 0.88070828 0.43721587</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -1.33169561 -0.00627653 1.02853908 -1.47952641</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] -1.9714967 -0.4147020 0.1369756 0.4128144 1.2403309 0.9644921</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.1369756 0.1369756 -1.3310188 0.6886533</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 1.02853908 -0.44976893 -0.98844311 0.88070828 0.88070828 0.43721587</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -1.33169561 -0.00627653 1.02853908 -1.47952641</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] 15 15 50 41 10 21 44 42 10 41</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 39 35 46 27 13 50 30 49 41 20</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] -0.8693350 -0.8693350 1.3196381 0.7567593 -1.1820455 -0.4940825</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.9443855 0.8193014 -1.1820455 0.7567593</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.3216338 0.0000000 0.8844928 -0.6432675 -1.7689857 1.2061266</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.4020422 1.1257182 0.4824506 -1.2061266</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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@@ -144,22 +145,22 @@
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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 26 >=4 0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B S 20 1 >=4</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C S 28 2 0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D S 26 <=0.25 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E S 23 2 0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F I 31 0.5 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G R 31 2 >=4</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H R 29 1 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I R 27 <=0.25 >=4</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J I 22 0.5 0.25</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 23 >=4 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B I 26 <=1 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C S 20 >=4 >=16</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D R 27 >=4 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E S 31 >=4 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F I 27 >=4 >=16</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G I 31 <=1 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H R 30 >=4 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I S 27 >=4 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J I 20 >=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> <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] -0.04047504 -0.25789134 -0.08826444 -0.63237868 -0.42488867 0.02453739</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 1.18267023 0.72772870 0.36605356 -0.85709171</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.12237407 -0.92897174 -0.07982527 0.24282355 0.22020411 0.34940813</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.12306945 0.80126097 0.09975463 -0.70395902</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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@@ -175,17 +176,17 @@
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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 S 28 2 0.25 -0.08826444 0.0000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 A S 26 >=4 0.25 -0.04047504 0.0477894</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 F I 31 0.5 1 0.02453739 0.1128018</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 B S 20 1 >=4 -0.25789134 0.1696269</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E S 23 2 0.25 -0.42488867 0.3366242</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 I R 27 <=0.25 >=4 0.36605356 0.4543180</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 D S 26 <=0.25 0.5 -0.63237868 0.5441142</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 J I 22 0.5 0.25 -0.85709171 0.7688273</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 H R 29 1 2 0.72772870 0.8159931</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 G R 31 2 >=4 1.18267023 1.2709347</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 20 >=4 >=16 -0.07982527 0.00000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 G I 31 <=1 8 -0.12306945 0.04324419</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 I S 27 >=4 4 0.09975463 0.17957990</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 A R 23 >=4 1 0.12237407 0.20219934</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E S 31 >=4 2 0.22020411 0.30002938</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 D R 27 >=4 0.5 0.24282355 0.32264882</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 F I 27 >=4 >=16 0.34940813 0.42923340</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 J I 20 >=4 0.5 -0.70395902 0.62413375</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 B I 26 <=1 0.5 -0.92897174 0.84914647</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 H R 30 >=4 4 0.80126097 0.88108624</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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