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Built site for AMR@2.1.1.9150: 9650545
This commit is contained in:
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@@ -7,7 +7,7 @@
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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="">2.1.1.9149</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9150</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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@@ -109,30 +109,30 @@
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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] R R S R S I R I R S</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] S R S S S R R R R 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] 0.9486833 0.9486833 -0.9486833 0.9486833 -0.9486833 -0.9486833</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.9486833 -0.9486833 0.9486833 -0.9486833</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -1.1618950 0.7745967 -1.1618950 -1.1618950 -1.1618950 0.7745967</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.7745967 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] 1 0.125 2 0.005 0.5 64 0.002 128 2 2 </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.005 0.25 1 2 >=16 8 1 1 0.025 4 </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] 0.0902697 -0.4972145 0.2860978 -1.4066119 -0.1055584 1.2652381</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -1.6654825 1.4610662 0.2860978 0.2860978</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -1.9714967 -0.4147020 0.1369756 0.4128144 1.2403309 0.9644921</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.1369756 0.1369756 -1.3310188 0.6886533</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] 0.0902697 -0.4972145 0.2860978 -1.4066119 -0.1055584 1.2652381</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -1.6654825 1.4610662 0.2860978 0.2860978</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -1.9714967 -0.4147020 0.1369756 0.4128144 1.2403309 0.9644921</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.1369756 0.1369756 -1.3310188 0.6886533</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] 48 19 18 10 16 48 41 6 26 24</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 15 15 50 41 10 21 44 42 10 41</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] 1.47901421 -0.43578097 -0.50180839 -1.03002776 -0.63386323 1.47901421</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 1.01682227 -1.29413744 0.02641097 -0.10564387</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.8693350 -0.8693350 1.3196381 0.7567593 -1.1820455 -0.4940825</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.9443855 0.8193014 -1.1820455 0.7567593</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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@@ -143,21 +143,21 @@
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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 S 22 <=0.25 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B I 24 4 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C S 21 4 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D I 18 1 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E R 26 4 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F R 22 0.5 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G I 23 4 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H S 23 2 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I S 27 <=0.25 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J R 25 4 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A S 26 >=4 0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B S 20 1 >=4</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C S 28 2 0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D S 26 <=0.25 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E S 23 2 0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F I 31 0.5 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G R 31 2 >=4</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H R 29 1 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I R 27 <=0.25 >=4</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J I 22 0.5 0.25</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> <span style="color: #0000BB;">ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",</span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;"> and "tobr"</span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.3343139 0.1355870 0.1534539 -0.7329889 0.8453491 -0.2831686</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.3456668 -0.4126742 -0.4661540 0.7492427</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.04047504 -0.25789134 -0.08826444 -0.63237868 -0.42488867 0.02453739</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 1.18267023 0.72772870 0.36605356 -0.85709171</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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@@ -174,16 +174,16 @@
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",</span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;"> and "tobr"</span></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 21 4 4 0.1534539 0.00000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B I 24 4 2 0.1355870 0.01786681</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 G I 23 4 4 0.3456668 0.19221294</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 F R 22 0.5 1 -0.2831686 0.43662245</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 A S 22 <=0.25 4 -0.3343139 0.48776774</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 H S 23 2 1 -0.4126742 0.56612805</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 J R 25 4 2 0.7492427 0.59578882</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 I S 27 <=0.25 1 -0.4661540 0.61960784</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 E R 26 4 2 0.8453491 0.69189529</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 D I 18 1 2 -0.7329889 0.88644273</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 C S 28 2 0.25 -0.08826444 0.0000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 A S 26 >=4 0.25 -0.04047504 0.0477894</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 F I 31 0.5 1 0.02453739 0.1128018</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 B S 20 1 >=4 -0.25789134 0.1696269</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E S 23 2 0.25 -0.42488867 0.3366242</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 I R 27 <=0.25 >=4 0.36605356 0.4543180</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 D S 26 <=0.25 0.5 -0.63237868 0.5441142</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 J I 22 0.5 0.25 -0.85709171 0.7688273</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 H R 29 1 2 0.72772870 0.8159931</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 G R 31 2 >=4 1.18267023 1.2709347</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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