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Built site for AMR: 1.8.2.9065@b1b7534
This commit is contained in:
@ -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="">1.8.2.9064</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9065</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] 0.125 0.025 0.25 2 0.01 1 0.002 64 4 >=128</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.025 0.005 0.01 4 4 8 1 >=16 0.001 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] -0.3838663 -0.8280016 -0.1925876 0.3812484 -1.0808583 0.1899697</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -1.5249937 1.3376418 0.5725271 1.5289205</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.6319520 -1.0956588 -0.8959511 0.8302930 0.8302930 1.0300007</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.4308777 1.2297083 -1.5593656 -0.1682452</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 2 2 <=1 16</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B 1 0.5 4 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C 8 2 2 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D 8 1 <=1 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E 4 <=0.025 2 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F 4 0.5 2 <=0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G 16 1 4 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 8 0.5 4 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I 4 0.0625 <=1 <=0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J 1 0.25 4 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 1 1 1 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B 1 2 8 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C 1 0.5 8 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D 1 1 16 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E 4 0.5 4 16</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F 4 1 1 16</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G 16 <=0.125 16 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 16 0.25 8 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I 4 1 8 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J 4 1 1 16</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] 0.21703198 0.23337558 0.25599565 0.09765543 -0.57494493 -0.29870099</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.85619568 0.29863042 -0.94854914 -0.13668968</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.55258772 -0.05081832 -0.65116115 -0.10941895 0.20887247 0.11308804</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.23423260 0.29283323 0.40187176 0.11308804</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> 9 I 4 0.0625 <=1 <=0.25 -0.94854914</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E 4 <=0.025 2 1 -0.57494493</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F 4 0.5 2 <=0.25 -0.29870099</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J 1 0.25 4 2 -0.13668968</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D 8 1 <=1 2 0.09765543</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A 2 2 <=1 16 0.21703198</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B 1 0.5 4 8 0.23337558</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C 8 2 2 0.5 0.25599565</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 8 0.5 4 0.5 0.29863042</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G 16 1 4 2 0.85619568</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 1 0.5 8 1 -0.65116115</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A 1 1 1 4 -0.55258772</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D 1 1 16 2 -0.10941895</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B 1 2 8 2 -0.05081832</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F 4 1 1 16 0.11308804</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J 4 1 1 16 0.11308804</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E 4 0.5 4 16 0.20887247</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G 16 <=0.125 16 8 0.23423260</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 16 0.25 8 8 0.29283323</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I 4 1 8 8 0.40187176</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 8 2 2 0.5 0.25599565 0.00000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B 1 0.5 4 8 0.23337558 0.02262008</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 A 2 2 <=1 16 0.21703198 0.03896367</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 H 8 0.5 4 0.5 0.29863042 0.04263477</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 D 8 1 <=1 2 0.09765543 0.15834022</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 J 1 0.25 4 2 -0.13668968 0.39268533</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 F 4 0.5 2 <=0.25 -0.29870099 0.55469664</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 G 16 1 4 2 0.85619568 0.60020002</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 E 4 <=0.025 2 1 -0.57494493 0.83094058</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 I 4 0.0625 <=1 <=0.25 -0.94854914 1.20454480</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 1 0.5 8 1 -0.65116115 0.00000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 A 1 1 1 4 -0.55258772 0.09857343</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 D 1 1 16 2 -0.10941895 0.54174220</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 B 1 2 8 2 -0.05081832 0.60034283</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 F 4 1 1 16 0.11308804 0.76424920</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 J 4 1 1 16 0.11308804 0.76424920</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 E 4 0.5 4 16 0.20887247 0.86003362</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 G 16 <=0.125 16 8 0.23423260 0.88539375</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 H 16 0.25 8 8 0.29283323 0.94399438</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 I 4 1 8 8 0.40187176 1.05303291</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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