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https://github.com/msberends/AMR.git
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Built site for AMR: 1.8.2.9142@e70f2cd
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="">1.8.2.9141</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9142</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 +201,30 @@
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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] S S S S I S S S R I</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] I R I R S R R I S 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] -0.3162278 -0.3162278 -0.3162278 -0.3162278 -0.3162278 -0.3162278</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.3162278 -0.3162278 2.8460499 -0.3162278</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.7745967 1.1618950 -0.7745967 1.1618950 -0.7745967 1.1618950</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 1.1618950 -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] 64 >=256 32 0.25 16 0.125 0.0625 8 0.005 4 </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 128 0.125 0.025 1 1 8 0.125 <=0.01 1 0.0625</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] 0.9653291 1.3622258 0.7668808 -0.6222574 0.5684325 -0.8207057</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -1.0191540 0.3699842 -1.7422712 0.1715359</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 2.0067688 -0.4415318 -1.0100096 0.2929584 0.2929584 1.0274486</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.4415318 -1.3336573 0.2929584 -0.6863619</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] 0.9653291 1.3622258 0.7668808 -0.6222574 0.5684325 -0.8207057</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -1.0191540 0.3699842 -1.7422712 0.1715359</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 2.0067688 -0.4415318 -1.0100096 0.2929584 0.2929584 1.0274486</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.4415318 -1.3336573 0.2929584 -0.6863619</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] 40 44 42 43 40 21 27 19 30 44</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 19 33 9 33 40 43 40 7 39 44</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] 0.5097207 0.9174973 0.7136090 0.8155532 0.5097207 -1.4272181</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.8155532 -1.6311064 -0.5097207 0.9174973</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.8390265 0.1649368 -1.5561432 0.1649368 0.6669185 0.8820535</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.6669185 -1.6995665 0.5952068 0.9537652</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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@ -235,21 +235,21 @@
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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 I 26 2 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B I 27 4 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C S 29 2 >=4</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D R 21 2 >=4</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E S 29 4 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F R 22 2 <=0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G R 22 >=8 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H I 29 4 <=0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I I 21 1 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J S 19 0.5 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A R 20 1 >=16</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B R 17 >=16 <=0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C I 22 2 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D R 18 >=16 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E S 25 8 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F I 18 1 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G I 28 4 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H R 19 >=16 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I R 21 1 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J I 18 8 8</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] -0.10301516 0.18138650 0.42497726 0.42897384 0.47747975 -0.17765248</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.76587798 -0.02563555 -0.81189821 -1.16049394</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.210274980 -0.189659861 -0.361042252 0.008770745 0.395772293</span>
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<span class="r-out co"><span class="r-pr">#></span> [6] -0.660927881 0.080327628 0.590266790 0.025640147 -0.099422589</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 +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 S 29 2 >=4 0.42497726 0.000000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 D R 21 2 >=4 0.42897384 0.003996578</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 E S 29 4 2 0.47747975 0.052502484</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 B I 27 4 1 0.18138650 0.243590762</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 G R 22 >=8 2 0.76587798 0.340900719</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 H I 29 4 <=0.25 -0.02563555 0.450612811</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 A I 26 2 1 -0.10301516 0.527992418</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 F R 22 2 <=0.25 -0.17765248 0.602629741</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I I 21 1 0.5 -0.81189821 1.236875468</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J S 19 0.5 0.5 -1.16049394 1.585471198</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 22 2 2 -0.361042252 0.0000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B R 17 >=16 <=0.25 -0.189659861 0.1713824</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 J I 18 8 8 -0.099422589 0.2616197</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 F I 18 1 4 -0.660927881 0.2998856</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 D R 18 >=16 0.5 0.008770745 0.3698130</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 I R 21 1 4 0.025640147 0.3866824</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G I 28 4 1 0.080327628 0.4413699</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 A R 20 1 >=16 0.210274980 0.5713172</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 E S 25 8 8 0.395772293 0.7568145</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 H R 19 >=16 8 0.590266790 0.9513090</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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