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https://github.com/msberends/AMR.git
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Built site for AMR: 1.8.2.9016@76bcd35
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="">1.8.2.9014</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9016</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] <=0.01 0.025 4 0.0625 1 4 16 0.5 0.025 8 </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.125 <=0.002 0.01 >=64 0.01 0.25 0.5 0.025 2 </span>
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<span class="r-out co"><span class="r-pr">#></span> [10] 0.125 </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] -1.4081939 -1.0706595 0.7988846 -0.7331250 0.2882147 0.7988846</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 1.3095545 0.0328798 -1.0706595 1.0542196</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.009782872 -1.384392080 -0.849383842 2.063956687 -0.849383842</span>
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<span class="r-out co"><span class="r-pr">#></span> [6] 0.220632635 0.451048141 -0.544791110 0.911879154 -0.009782872</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 4 <=0.025 <=1 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B 2 0.125 2 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C 32 <=0.025 16 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D 2 2 <=1 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E 32 1 8 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F 1 0.125 2 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G 4 0.5 16 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 2 1 <=1 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I 8 0.125 <=1 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J 1 >=4 4 16</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 32 2 1 >=16</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B >=64 0.25 4 >=16</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C 16 0.0625 <=0.5 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D 16 0.5 <=0.5 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E <=2 2 16 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F >=64 0.25 8 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G 16 0.0625 8 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 4 1 4 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I <=2 4 16 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J 32 2 16 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] -0.77937382 -0.36771977 0.74573282 -0.12706157 0.43836890 -0.50465041</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.41987005 -0.39451457 -0.07597364 0.64532202</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.4639259 0.4984972 -1.0321239 -0.3551673 0.2661953 0.2953882</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.2040150 -0.1307227 -0.1096856 0.3077079</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> 1 A 4 <=0.025 <=1 1 -0.77937382</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F 1 0.125 2 2 -0.50465041</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 2 1 <=1 1 -0.39451457</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B 2 0.125 2 2 -0.36771977</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D 2 2 <=1 2 -0.12706157</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I 8 0.125 <=1 4 -0.07597364</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G 4 0.5 16 2 0.41987005</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E 32 1 8 0.5 0.43836890</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J 1 >=4 4 16 0.64532202</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C 32 <=0.025 16 8 0.74573282</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 16 0.0625 <=0.5 1 -1.0321239</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D 16 0.5 <=0.5 4 -0.3551673</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G 16 0.0625 8 4 -0.2040150</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 4 1 4 4 -0.1307227</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I <=2 4 16 1 -0.1096856</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E <=2 2 16 8 0.2661953</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F >=64 0.25 8 4 0.2953882</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J 32 2 16 1 0.3077079</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A 32 2 1 >=16 0.4639259</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B >=64 0.25 4 >=16 0.4984972</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 32 <=0.025 16 8 0.74573282 0.0000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 J 1 >=4 4 16 0.64532202 0.1004108</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 E 32 1 8 0.5 0.43836890 0.3073639</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 G 4 0.5 16 2 0.41987005 0.3258628</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 I 8 0.125 <=1 4 -0.07597364 0.8217065</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 D 2 2 <=1 2 -0.12706157 0.8727944</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 B 2 0.125 2 2 -0.36771977 1.1134526</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 2 1 <=1 1 -0.39451457 1.1402474</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 F 1 0.125 2 2 -0.50465041 1.2503832</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 A 4 <=0.025 <=1 1 -0.77937382 1.5251066</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 0.0625 <=0.5 1 -1.0321239 0.0000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 D 16 0.5 <=0.5 4 -0.3551673 0.6769567</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 G 16 0.0625 8 4 -0.2040150 0.8281090</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 H 4 1 4 4 -0.1307227 0.9014012</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 I <=2 4 16 1 -0.1096856 0.9224383</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 E <=2 2 16 8 0.2661953 1.2983192</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 F >=64 0.25 8 4 0.2953882 1.3275121</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 J 32 2 16 1 0.3077079 1.3398318</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 A 32 2 1 >=16 0.4639259 1.4960498</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 B >=64 0.25 4 >=16 0.4984972 1.5306211</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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