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https://github.com/msberends/AMR.git
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Built site for AMR: 1.8.2.9064@23fe427
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="">1.8.2.9063</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9064</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] 1 0.0625 0.001 0.001 0.5 0.5 0.125 32 0.125 32 </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-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] 0.4278030 -0.3524476 -1.5161494 -1.5161494 0.2327404 0.2327404</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.1573850 1.4031163 -0.1573850 1.4031163</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-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 8 4 >=16 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B 8 0.25 0.5 0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C 16 0.25 0.25 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D 16 4 0.5 0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E >=32 1 0.5 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F 8 <=0.125 >=16 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G 16 0.25 1 0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 4 0.5 4 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I 16 4 0.25 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J 8 0.25 1 8</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-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] 0.877285110 -0.776502449 -0.356795921 0.029167509 0.657578311</span>
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<span class="r-out co"><span class="r-pr">#></span> [6] 0.001921626 -0.371866780 -0.139430735 0.154699834 -0.076056506</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-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> 2 B 8 0.25 0.5 0.25 -0.776502449</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G 16 0.25 1 0.25 -0.371866780</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C 16 0.25 0.25 1 -0.356795921</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 4 0.5 4 4 -0.139430735</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J 8 0.25 1 8 -0.076056506</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F 8 <=0.125 >=16 2 0.001921626</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D 16 4 0.5 0.25 0.029167509</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I 16 4 0.25 1 0.154699834</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E >=32 1 0.5 8 0.657578311</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A 8 4 >=16 8 0.877285110</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-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 16 0.25 0.25 1 -0.356795921 0.00000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 G 16 0.25 1 0.25 -0.371866780 0.01507086</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 H 4 0.5 4 4 -0.139430735 0.21736519</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 J 8 0.25 1 8 -0.076056506 0.28073941</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 F 8 <=0.125 >=16 2 0.001921626 0.35871755</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 D 16 4 0.5 0.25 0.029167509 0.38596343</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 B 8 0.25 0.5 0.25 -0.776502449 0.41970653</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 I 16 4 0.25 1 0.154699834 0.51149575</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 E >=32 1 0.5 8 0.657578311 1.01437423</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 A 8 4 >=16 8 0.877285110 1.23408103</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-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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