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Built site for AMR: 1.8.2.9057@ac55aa8
This commit is contained in:
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@ -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="">1.8.2.9054</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9057</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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@ -200,10 +200,10 @@
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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] 0.5 32 1 4 256 64 4 0.002 0.025 0.5 </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.125 16 128 0.5 4 0.5 0.0625 0.01 0.025 32 </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] -0.3241709 0.8396588 -0.1301993 0.2577439 1.4215736 1.0336304</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.2577439 -1.8693070 -1.1625023 -0.3241709</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.5844196 0.9288246 1.5773579 -0.1520641 0.4964691 -0.1520641</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.8005973 -1.3721402 -1.0863687 1.1450024</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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@ -213,38 +213,38 @@
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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 <=0.125 <=0.5 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B 4 0.25 1 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C 32 0.25 1 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D 2 <=0.125 <=0.5 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E 8 <=0.125 8 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F 32 0.25 2 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G 8 0.5 1 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 2 >=1 8 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I 32 <=0.125 4 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J 16 0.25 2 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 16 >=4 1 >=8</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B 8 1 1 >=8</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C 8 2 4 <=0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D 8 0.25 16 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E 4 <=0.0625 4 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F 16 1 2 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G 8 2 4 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 4 1 4 >=8</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I 4 0.5 4 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J 16 0.125 1 <=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> "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] -0.51912782 -0.09831951 0.63538430 -1.20290099 -0.21181627 0.27774576</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.04628481 0.49245479 0.45927606 0.12101887</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.58580073 0.01609138 -0.12243892 0.37435404 -0.58927461 0.35318445</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.37571945 0.10382446 -0.36004270 -0.73721828</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> 4 D 2 <=0.125 <=0.5 1 -1.20290099</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A 4 <=0.125 <=0.5 4 -0.51912782</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E 8 <=0.125 8 1 -0.21181627</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B 4 0.25 1 4 -0.09831951</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G 8 0.5 1 2 0.04628481</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J 16 0.25 2 2 0.12101887</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F 32 0.25 2 2 0.27774576</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I 32 <=0.125 4 4 0.45927606</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 2 >=1 8 2 0.49245479</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C 32 0.25 1 8 0.63538430</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> 10 J 16 0.125 1 <=0.5 -0.73721828</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E 4 <=0.0625 4 4 -0.58927461</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I 4 0.5 4 2 -0.36004270</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C 8 2 4 <=0.5 -0.12243892</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B 8 1 1 >=8 0.01609138</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 4 1 4 >=8 0.10382446</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F 16 1 2 4 0.35318445</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D 8 0.25 16 4 0.37435404</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G 8 2 4 4 0.37571945</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A 16 >=4 1 >=8 0.58580073</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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@ -256,17 +256,17 @@
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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 0.25 1 8 0.63538430 0.0000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 H 2 >=1 8 2 0.49245479 0.1429295</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 I 32 <=0.125 4 4 0.45927606 0.1761082</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 F 32 0.25 2 2 0.27774576 0.3576385</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 J 16 0.25 2 2 0.12101887 0.5143654</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 G 8 0.5 1 2 0.04628481 0.5890995</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 B 4 0.25 1 4 -0.09831951 0.7337038</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 E 8 <=0.125 8 1 -0.21181627 0.8472006</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 A 4 <=0.125 <=0.5 4 -0.51912782 1.1545121</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 D 2 <=0.125 <=0.5 1 -1.20290099 1.8382853</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 8 2 4 <=0.5 -0.12243892 0.0000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B 8 1 1 >=8 0.01609138 0.1385303</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 H 4 1 4 >=8 0.10382446 0.2262634</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 I 4 0.5 4 2 -0.36004270 0.2376038</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E 4 <=0.0625 4 4 -0.58927461 0.4668357</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F 16 1 2 4 0.35318445 0.4756234</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 D 8 0.25 16 4 0.37435404 0.4967930</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 G 8 2 4 4 0.37571945 0.4981584</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 J 16 0.125 1 <=0.5 -0.73721828 0.6147794</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 A 16 >=4 1 >=8 0.58580073 0.7082397</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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