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https://github.com/msberends/AMR.git
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Built site for AMR: 1.8.2.9024@aa2c063
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="">1.8.2.9023</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9024</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] 1 >=128 >=128 0.001 4 0.125 0.25 0.01 0.001 2 </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 4 128 2 4 256 <=0.001 <=0.001 4 1 </span>
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<span class="r-out co"><span class="r-pr">#></span> [10] 0.01 </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] 0.23800503 1.38104904 1.38104904 -1.38932783 0.56458903 -0.25187098</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.08857897 -0.84688355 -1.38932783 0.40129703</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.38501534 1.16834939 0.22834853 0.38501534 1.32501620 -1.48962591</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -1.48962591 0.38501534 0.07168172 -0.96919003</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 16 <=0.025 >=4 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B 4 0.5 1 <=0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C 4 0.0625 1 <=0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D >=32 1 >=4 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E 4 0.125 2 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F 8 0.0625 >=4 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G 4 0.0625 2 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H >=32 0.0625 1 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I 8 0.25 <=0.25 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J >=32 0.0625 <=0.25 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 4 0.25 1 >=16</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B <=2 >=2 1 <=1</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C <=2 0.025 0.5 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D 4 >=2 4 <=1</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E >=16 0.025 4 >=16</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F >=16 0.125 0.5 >=16</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G <=2 >=2 0.25 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H <=2 0.025 2 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I >=16 0.0625 0.25 <=1</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J 8 0.025 4 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> "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] -0.14091001 -0.32396107 -0.78118181 0.85710543 0.08049237 0.41685866</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.07191455 0.18697943 -0.07834229 -0.14512615</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.2679478 -0.2300449 -0.6609425 0.2703257 0.6591997 0.3959389</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.1096818 -0.4920944 -0.4283259 0.3276773</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> 3 C 4 0.0625 1 <=0.25 -0.78118181</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B 4 0.5 1 <=0.25 -0.32396107</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J >=32 0.0625 <=0.25 2 -0.14512615</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A 16 <=0.025 >=4 0.5 -0.14091001</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I 8 0.25 <=0.25 4 -0.07834229</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G 4 0.0625 2 4 -0.07191455</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E 4 0.125 2 4 0.08049237</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H >=32 0.0625 1 2 0.18697943</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F 8 0.0625 >=4 8 0.41685866</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D >=32 1 >=4 0.5 0.85710543</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> 3 C <=2 0.025 0.5 4 -0.6609425</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H <=2 0.025 2 2 -0.4920944</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I >=16 0.0625 0.25 <=1 -0.4283259</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B <=2 >=2 1 <=1 -0.2300449</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G <=2 >=2 0.25 8 -0.1096818</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A 4 0.25 1 >=16 0.2679478</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D 4 >=2 4 <=1 0.2703257</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J 8 0.025 4 8 0.3276773</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F >=16 0.125 0.5 >=16 0.3959389</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E >=16 0.025 4 >=16 0.6591997</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 4 0.0625 1 <=0.25 -0.78118181 0.0000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B 4 0.5 1 <=0.25 -0.32396107 0.4572207</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 J >=32 0.0625 <=0.25 2 -0.14512615 0.6360557</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 A 16 <=0.025 >=4 0.5 -0.14091001 0.6402718</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 I 8 0.25 <=0.25 4 -0.07834229 0.7028395</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 G 4 0.0625 2 4 -0.07191455 0.7092673</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 E 4 0.125 2 4 0.08049237 0.8616742</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H >=32 0.0625 1 2 0.18697943 0.9681612</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 F 8 0.0625 >=4 8 0.41685866 1.1980405</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 D >=32 1 >=4 0.5 0.85710543 1.6382872</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 <=2 0.025 0.5 4 -0.6609425 0.0000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 H <=2 0.025 2 2 -0.4920944 0.1688482</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 I >=16 0.0625 0.25 <=1 -0.4283259 0.2326166</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 B <=2 >=2 1 <=1 -0.2300449 0.4308977</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 G <=2 >=2 0.25 8 -0.1096818 0.5512607</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 A 4 0.25 1 >=16 0.2679478 0.9288903</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 D 4 >=2 4 <=1 0.2703257 0.9312683</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 J 8 0.025 4 8 0.3276773 0.9886199</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 F >=16 0.125 0.5 >=16 0.3959389 1.0568815</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 E >=16 0.025 4 >=16 0.6591997 1.3201423</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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