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Built site for AMR: 1.8.2.9150@7ad8635
This commit is contained in:
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@@ -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="">1.8.2.9148</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9150</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 +201,31 @@
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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 I I I I S R S I R</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] S I S R I I S 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] 1.449138 -0.621059 -0.621059 -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 1.449138</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.4743416 -0.4743416 -0.4743416 1.8973666 -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 -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] 0.25 1 8 <=0.005 <=0.005 2 0.01 >=256 16 </span>
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<span class="r-out co"><span class="r-pr">#></span> [10] 8 </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.0625 <=0.001 0.0625 128 0.0625 64 256 8 0.0625 </span>
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<span class="r-out co"><span class="r-pr">#></span> [10] 0.002 </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] -0.27951091 0.09147782 0.64796092 -1.32641444 -1.32641444 0.27697218</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -1.14092007 1.57543274 0.83345528 0.64796092</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.4417215 -1.3482772 -0.4417215 1.2298295 -0.4417215 1.0778703</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 1.3817887 0.6219928 -0.4417215 -1.1963180</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] -0.27951091 0.09147782 0.64796092 -1.32641444 -1.32641444 0.27697218</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -1.14092007 1.57543274 0.83345528 0.64796092</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.4417215 -1.3482772 -0.4417215 1.2298295 -0.4417215 1.0778703</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 1.3817887 0.6219928 -0.4417215 -1.1963180</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] 42 21 38 40 46 49 41 15 29 48</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 8 43 46 31 33 33 37 43 45 27</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] 0.44150742 -1.37646431 0.09522709 0.26836726 0.78778775 1.04749800</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.35493734 -1.89588481 -0.68390365 0.96092792</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -2.3345712 0.7372330 1.0005305 -0.3159570 -0.1404253 -0.1404253</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.2106380 0.7372330 0.9127647 -0.6670203</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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@@ -236,21 +236,21 @@
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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 R 17 0.5 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B I 22 4 >=8</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C R 31 1 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D R 23 1 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E R 29 1 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F I 21 1 >=8</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G R 19 0.5 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H S 20 0.5 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I R 22 2 <=0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J S 19 2 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A R 29 >=8 <=0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B S 31 1 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C S 27 >=8 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D R 25 2 <=0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E R 27 0.5 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F I 22 0.5 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G R 22 0.5 16</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H I 23 4 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I S 27 0.5 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J R 20 4 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] -0.55862477 0.58537655 0.77602663 0.17820212 0.51539668 0.02637631</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.44622659 -0.72591865 0.07694007 -0.42754836</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.487327335 0.218326088 0.247132119 -0.092191622 0.008553263</span>
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<span class="r-out co"><span class="r-pr">#></span> [6] -0.823174446 0.153968346 0.065818788 -0.465788386 0.200028515</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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@@ -267,16 +267,16 @@
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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 31 1 2 0.77602663 0.0000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B I 22 4 >=8 0.58537655 0.1906501</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 E R 29 1 1 0.51539668 0.2606300</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D R 23 1 1 0.17820212 0.5978245</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 I R 22 2 <=0.25 0.07694007 0.6990866</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F I 21 1 >=8 0.02637631 0.7496503</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 J S 19 2 0.5 -0.42754836 1.2035750</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 G R 19 0.5 0.5 -0.44622659 1.2222532</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 A R 17 0.5 0.5 -0.55862477 1.3346514</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 H S 20 0.5 1 -0.72591865 1.5019453</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 C S 27 >=8 2 0.247132119 0.00000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B S 31 1 4 0.218326088 0.02880603</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 J R 20 4 4 0.200028515 0.04710360</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 G R 22 0.5 16 0.153968346 0.09316377</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 H I 23 4 8 0.065818788 0.18131333</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 E R 27 0.5 1 0.008553263 0.23857886</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 A R 29 >=8 <=0.25 0.487327335 0.24019522</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 D R 25 2 <=0.25 -0.092191622 0.33932374</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I S 27 0.5 1 -0.465788386 0.71292051</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 F I 22 0.5 1 -0.823174446 1.07030656</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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