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https://github.com/msberends/AMR.git
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Built site for AMR: 2.0.0.9002@dd7cc86
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="">2.0.0</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9002</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 +201,31 @@
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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] I S S R S S I S R R</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] R I I R S I I I S R</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] -0.621059 -0.621059 -0.621059 1.449138 -0.621059 -0.621059 -0.621059</span>
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<span class="r-out co"><span class="r-pr">#></span> [8] -0.621059 1.449138 1.449138</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 1.449138 -0.621059 -0.621059 1.449138 -0.621059 -0.621059 -0.621059</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-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] 0.002 0.125 0.001 16 16 64 2 16 0.5 0.0625</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 2 0.0625 0.5 <=0.025 1 <=0.025 2 0.5 <=0.025</span>
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<span class="r-out co"><span class="r-pr">#></span> [10] >=256 </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] -1.45381664 -0.39257207 -1.63170516 0.85264760 0.85264760 1.20842465</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.31898203 0.85264760 -0.03679502 -0.57046060</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.52989759 -0.67629105 0.04742213 -0.99518998 0.28865986 -0.99518998</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.52989759 0.04742213 -0.99518998 2.21856169</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] -1.45381664 -0.39257207 -1.63170516 0.85264760 0.85264760 1.20842465</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.31898203 0.85264760 -0.03679502 -0.57046060</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.52989759 -0.67629105 0.04742213 -0.99518998 0.28865986 -0.99518998</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.52989759 0.04742213 -0.99518998 2.21856169</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] 41 7 31 43 26 15 50 45 50 36</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 36 41 38 14 14 46 22 45 45 40</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] 0.4508859 -1.8718595 -0.2322745 0.5875180 -0.5738547 -1.3253312</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 1.0657302 0.7241500 1.0657302 0.1093057</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.1504749 0.5464614 0.3088695 -1.5918660 -1.5918660 0.9424480</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.9582875 0.8632507 0.8632507 0.4672641</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 +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 25 >=2 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B I 29 >=2 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C S 30 >=2 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D R 22 >=2 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E R 21 1 0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F R 28 >=2 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G R 20 1 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H I 19 >=2 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I S 30 1 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J R 27 >=2 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A S 30 8 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B S 30 2 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C R 27 8 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D I 17 <=1 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E I 28 <=1 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F R 27 4 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G I 25 4 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H S 19 4 0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I I 18 <=1 0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J S 26 2 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">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] 0.65477694 0.24022002 -0.02948384 0.47956157 -0.75261068 0.50188332</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.64696131 -0.67194018 -0.05486954 0.27942371</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.51643016 -0.02872404 1.19466519 -0.54741122 -0.34374818 0.98167950</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.28671398 -0.61531550 -1.09230611 -0.35198377</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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@ -266,16 +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 S 30 >=2 0.5 -0.02948384 0.0000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 I S 30 1 4 -0.05486954 0.0253857</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 B I 29 >=2 2 0.24022002 0.2697039</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 J R 27 >=2 0.5 0.27942371 0.3089076</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 D R 22 >=2 4 0.47956157 0.5090454</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F R 28 >=2 1 0.50188332 0.5313672</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G R 20 1 0.5 -0.64696131 0.6174775</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H I 19 >=2 0.5 -0.67194018 0.6424563</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 A R 25 >=2 4 0.65477694 0.6842608</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 E R 21 1 0.25 -0.75261068 0.7231268</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 C R 27 8 8 1.19466519 0.0000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 F R 27 4 8 0.98167950 0.2129857</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 A S 30 8 2 0.51643016 0.6782350</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 G I 25 4 8 0.28671398 0.9079512</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 B S 30 2 1 -0.02872404 1.2233892</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 E I 28 <=1 1 -0.34374818 1.5384134</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 J S 26 2 0.5 -0.35198377 1.5466490</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 D I 17 <=1 8 -0.54741122 1.7420764</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 H S 19 4 0.25 -0.61531550 1.8099807</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 I I 18 <=1 0.25 -1.09230611 2.2869713</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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