mirror of
https://github.com/msberends/AMR.git
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Built site for AMR: 1.8.2.9034@6ad7857
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="">1.8.2.9033</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9034</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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@ -195,10 +195,11 @@
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<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">x</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">x</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] 4 0.0625 8 64 2 0.25 2 0.002 4 128 </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 128 0.002 0.125 0.01 128 0.25 0.005 0.25 <=0.001</span>
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<span class="r-out co"><span class="r-pr">#></span> [10] 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">x</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.27543358 -0.99915301 0.48786468 1.12515798 0.06300248 -0.57429082</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.06300248 -2.05404003 0.27543358 1.33758907</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 1.61986500 -1.04034961 -0.04633226 -0.65347059 1.61986500 0.12028746</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.82009031 0.12028746 -1.20696934 0.28690719</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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@ -208,38 +209,38 @@
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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 <=2 0.25 4 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B 4 1 0.25 <=1</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C >=16 0.125 4 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D <=2 0.5 1 >=4</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E 4 <=0.025 0.25 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F >=16 <=0.025 4 <=1</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G >=16 0.125 0.25 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 4 4 0.25 >=4</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I >=16 <=0.025 2 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J >=16 1 4 2</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 8 0.125 0.5 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B 32 0.25 2 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C 16 0.5 0.5 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D 32 1 >=4 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E 8 0.25 2 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F 64 0.0625 1 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G <=4 0.125 1 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 16 0.125 >=4 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I 16 0.5 0.5 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J 8 >=4 0.25 <=1</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> "id" and "tobr"</span>
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<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>NAs introduced by coercion</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.06445907 -0.57768610 0.40775164 0.14648310 -0.72133558 -0.19353229</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.11527439 0.36722427 0.05071121 0.70011720</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.72781282 0.45495874 0.28152212 0.92036634 0.29609879 -0.06040618</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.75419100 0.28709631 -0.23602705 -0.46160524</span>
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<span class="r-in"><span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span> <span class="op"><-</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span>, <span class="fu">where</span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span><span class="op">)</span></span></span>
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<span class="r-msg co"><span class="r-pr">#></span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent" and</span>
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<span class="r-msg co"><span class="r-pr">#></span> "tobr"</span>
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<span class="r-in"><span><span class="va">y</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/order.html" class="external-link">order</a></span><span class="op">(</span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span><span class="op">)</span>, <span class="op">]</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr amr_distance</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E 4 <=0.025 0.25 2 -0.72133558</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B 4 1 0.25 <=1 -0.57768610</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F >=16 <=0.025 4 <=1 -0.19353229</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G >=16 0.125 0.25 2 -0.11527439</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A <=2 0.25 4 2 -0.06445907</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I >=16 <=0.025 2 2 0.05071121</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D <=2 0.5 1 >=4 0.14648310</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 4 4 0.25 >=4 0.36722427</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C >=16 0.125 4 2 0.40775164</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J >=16 1 4 2 0.70011720</span>
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<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr amr_distance</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G <=4 0.125 1 2 -0.75419100</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A 8 0.125 0.5 2 -0.72781282</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J 8 >=4 0.25 <=1 -0.46160524</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I 16 0.5 0.5 2 -0.23602705</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F 64 0.0625 1 2 -0.06040618</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C 16 0.5 0.5 8 0.28152212</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 16 0.125 >=4 4 0.28709631</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E 8 0.25 2 8 0.29609879</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B 32 0.25 2 4 0.45495874</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D 32 1 >=4 4 0.92036634</span>
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<span class="r-in"><span></span></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="va">y</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
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@ -251,17 +252,17 @@
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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" and</span>
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<span class="r-msg co"><span class="r-pr">#></span> "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 >=16 0.125 4 2 0.40775164 0.00000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 H 4 4 0.25 >=4 0.36722427 0.04052737</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 D <=2 0.5 1 >=4 0.14648310 0.26126854</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 J >=16 1 4 2 0.70011720 0.29236555</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 I >=16 <=0.025 2 2 0.05071121 0.35704044</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 A <=2 0.25 4 2 -0.06445907 0.47221071</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G >=16 0.125 0.25 2 -0.11527439 0.52302603</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 F >=16 <=0.025 4 <=1 -0.19353229 0.60128393</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 B 4 1 0.25 <=1 -0.57768610 0.98543774</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 E 4 <=0.025 0.25 2 -0.72133558 1.12908723</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 16 0.5 0.5 8 0.28152212 0.000000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 H 16 0.125 >=4 4 0.28709631 0.005574198</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 E 8 0.25 2 8 0.29609879 0.014576672</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 B 32 0.25 2 4 0.45495874 0.173436622</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 F 64 0.0625 1 2 -0.06040618 0.341928295</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 I 16 0.5 0.5 2 -0.23602705 0.517549170</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 D 32 1 >=4 4 0.92036634 0.638844222</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 J 8 >=4 0.25 <=1 -0.46160524 0.743127361</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 A 8 0.125 0.5 2 -0.72781282 1.009334941</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 G <=4 0.125 1 2 -0.75419100 1.035713113</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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