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https://github.com/msberends/AMR.git
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Built site for AMR: 2.1.1.9003@7059568
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="">2.1.1.9002</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9003</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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@ -218,30 +218,30 @@
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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 S R S I I R I I S</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] R S I I S R I S I 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] 1.449138 -0.621059 1.449138 -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 -0.621059 -0.621059</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 1.8973666 -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] -0.4743416 -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] 0.125 0.0625 1 8 4 0.25 >=32 0.5 0.005 0.25 </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 16 8 32 0.0625 0.5 >=256 0.002 0.001 1 0.005 </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] -0.554873825 -0.827456801 0.262875102 1.080624029 0.808041053</span>
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<span class="r-out co"><span class="r-pr">#></span> [6] -0.282290850 1.625789980 -0.009707874 -1.820709964 -0.282290850</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.82035688 0.66129723 0.97941652 -0.45212029 0.02505865 1.45659546</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -1.24197617 -1.40103582 0.18411830 -1.03171076</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] -0.554873825 -0.827456801 0.262875102 1.080624029 0.808041053</span>
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<span class="r-out co"><span class="r-pr">#></span> [6] -0.282290850 1.625789980 -0.009707874 -1.820709964 -0.282290850</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.82035688 0.66129723 0.97941652 -0.45212029 0.02505865 1.45659546</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -1.24197617 -1.40103582 0.18411830 -1.03171076</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] 26 32 50 20 28 49 12 20 9 42</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 7 15 31 28 22 45 13 21 18 41</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] -0.19375217 0.22143105 1.46698069 -0.60893538 -0.05535776 1.39778349</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -1.16251300 -0.60893538 -1.37010461 0.91340307</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -1.4040837 -0.7472024 0.5665601 0.3202296 -0.1724313 1.7161023</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.9114228 -0.2545415 -0.5008720 1.3876617</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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@ -251,22 +251,22 @@
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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 23 >=4 <=2</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B S 27 1 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C I 26 >=4 <=2</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D I 19 1 >=16</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E S 20 2 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F I 25 0.5 >=16</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G S 18 0.5 <=2</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H R 19 2 >=16</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I R 22 1 <=2</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J R 20 0.5 8</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 28 >=16 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B I 31 1 >=8</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C R 23 8 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D R 25 >=16 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E I 17 >=16 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F I 22 8 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G S 17 8 <=0.25</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 19 8 <=0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J R 19 <=0.5 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> 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] 0.05387469 0.12082470 0.28731436 -0.12784750 -0.20825803 0.12342200</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.98202095 0.60531151 0.06239096 0.06498826</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.64013819 0.32815059 0.24520983 0.61863348 -0.14954667 0.11665680</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.69000290 -0.43800225 -0.58498190 -0.08625517</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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@ -282,17 +282,17 @@
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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 26 >=4 <=2 0.28731436 0.0000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 F I 25 0.5 >=16 0.12342200 0.1638924</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 B S 27 1 4 0.12082470 0.1664897</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 J R 20 0.5 8 0.06498826 0.2223261</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 I R 22 1 <=2 0.06239096 0.2249234</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 A S 23 >=4 <=2 0.05387469 0.2334397</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 H R 19 2 >=16 0.60531151 0.3179971</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 D I 19 1 >=16 -0.12784750 0.4151619</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 E S 20 2 4 -0.20825803 0.4955724</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 G S 18 0.5 <=2 -0.98202095 1.2693353</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 23 8 0.5 0.24520983 0.00000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B I 31 1 >=8 0.32815059 0.08294076</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 F I 22 8 4 0.11665680 0.12855303</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 J R 19 <=0.5 4 -0.08625517 0.33146500</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 D R 25 >=16 1 0.61863348 0.37342365</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 E I 17 >=16 2 -0.14954667 0.39475650</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 A R 28 >=16 0.5 0.64013819 0.39492836</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H S 19 1 4 -0.43800225 0.68321208</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I S 19 8 <=0.25 -0.58498190 0.83019173</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 G S 17 8 <=0.25 -0.69000290 0.93521273</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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