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Built site for AMR: 1.8.2.9022@fed3b64
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="">1.8.2.9021</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9022</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 +195,10 @@
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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] 256 0.005 0.25 0.001 0.005 8 0.0625 64 0.002 0.125 </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] >=8 0.01 0.002 0.25 1 0.5 0.001 >=8 2 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">x</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 1.66607429 -0.78770118 0.09755088 -1.15190103 -0.78770118 0.88181258</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.21615380 1.35236960 -0.99504869 -0.05930146</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 1.017806264 -0.962121752 -1.438824265 -0.008716725 0.401892471</span>
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<span class="r-out co"><span class="r-pr">#></span> [6] 0.196587873 -1.644128863 1.017806264 0.607197068 0.812501666</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 +208,38 @@
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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 8 0.5 16 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B 8 1 2 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C 4 2 16 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D 16 0.25 2 <=0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E 16 2 2 <=0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F 8 2 4 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G 4 2 1 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 16 0.25 1 <=0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I 16 0.25 2 <=0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J 4 0.5 2 1</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 0.5 <=1 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B >=64 0.25 >=8 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C >=64 0.25 4 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D 16 0.25 <=1 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E 32 >=1 >=8 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F 16 >=1 <=1 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G <=2 0.5 <=1 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H <=2 <=0.125 2 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I >=64 0.25 <=1 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J >=64 0.25 <=1 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] 0.39410626 0.30081422 0.60129626 -0.39562183 0.15997607 0.53807346</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.09618958 -0.56999329 -0.39562183 -0.53683974</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.7016722 0.7163537 0.3902942 -0.6197198 1.1177827 0.0265375</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.1746259 -1.0218701 0.1334600 0.1334600</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> 8 H 16 0.25 1 <=0.25 -0.56999329</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J 4 0.5 2 1 -0.53683974</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D 16 0.25 2 <=0.25 -0.39562183</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I 16 0.25 2 <=0.25 -0.39562183</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G 4 2 1 4 -0.09618958</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E 16 2 2 <=0.25 0.15997607</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B 8 1 2 8 0.30081422</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A 8 0.5 16 2 0.39410626</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F 8 2 4 4 0.53807346</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C 4 2 16 4 0.60129626</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> 8 H <=2 <=0.125 2 0.5 -1.0218701</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A <=2 0.5 <=1 0.5 -0.7016722</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D 16 0.25 <=1 0.5 -0.6197198</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G <=2 0.5 <=1 8 -0.1746259</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F 16 >=1 <=1 1 0.0265375</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I >=64 0.25 <=1 8 0.1334600</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J >=64 0.25 <=1 8 0.1334600</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C >=64 0.25 4 4 0.3902942</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B >=64 0.25 >=8 8 0.7163537</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E 32 >=1 >=8 8 1.1177827</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 +251,17 @@
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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 2 16 4 0.60129626 0.0000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 F 8 2 4 4 0.53807346 0.0632228</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 A 8 0.5 16 2 0.39410626 0.2071900</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 B 8 1 2 8 0.30081422 0.3004820</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E 16 2 2 <=0.25 0.15997607 0.4413202</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 G 4 2 1 4 -0.09618958 0.6974858</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 D 16 0.25 2 <=0.25 -0.39562183 0.9969181</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 I 16 0.25 2 <=0.25 -0.39562183 0.9969181</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 J 4 0.5 2 1 -0.53683974 1.1381360</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 H 16 0.25 1 <=0.25 -0.56999329 1.1712895</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 >=64 0.25 4 4 0.3902942 0.0000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 I >=64 0.25 <=1 8 0.1334600 0.2568343</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 J >=64 0.25 <=1 8 0.1334600 0.2568343</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 B >=64 0.25 >=8 8 0.7163537 0.3260595</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 F 16 >=1 <=1 1 0.0265375 0.3637567</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 G <=2 0.5 <=1 8 -0.1746259 0.5649201</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 E 32 >=1 >=8 8 1.1177827 0.7274885</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 D 16 0.25 <=1 0.5 -0.6197198 1.0100140</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 A <=2 0.5 <=1 0.5 -0.7016722 1.0919664</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 H <=2 <=0.125 2 0.5 -1.0218701 1.4121643</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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