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Built site for AMR: 1.8.2.9054@ba51c2d
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="">1.8.2.9053</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9054</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] 0.002 0.5 0.005 0.005 1 0.005 32 0.0625 1 >=64 </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 64 1 8 0.025 0.002 0.005 0.0625 16 0.01 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] -1.1714935 0.2920876 -0.9286111 -0.9286111 0.4758210 -0.9286111</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 1.3944883 -0.2591128 0.4758210 1.5782217</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 1.3091844 0.2558741 0.7825293 -0.6783995 -1.3180848 -1.0860180</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.4463328 0.9580810 -0.9104663 1.1336327</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 16 0.0625 4 <=0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B 4 4 8 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C 32 2 0.5 <=0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D 32 2 2 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E 16 4 8 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F 16 1 8 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G 4 0.125 1 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H <=2 0.5 >=16 <=0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I 32 1 4 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J 16 1 4 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 8 0.025 1 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B <=4 0.125 0.5 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C <=4 >=1 4 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D <=4 0.125 1 >=8</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E >=16 >=1 2 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F >=16 0.025 1 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G <=4 0.25 4 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H >=16 0.125 0.5 >=8</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I 8 0.5 0.5 >=8</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J <=4 0.25 1 1</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] -0.69810970 0.10645099 -0.38692709 0.41316947 0.69213408 0.44073351</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.54222633 -0.51743382 0.45152367 0.04068523</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.55426393 -0.42949279 0.62941387 -0.05490015 0.49015830 -0.12782528</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.09926391 0.26899945 0.26246847 -0.38529402</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> 1 A 16 0.0625 4 <=0.5 -0.69810970</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G 4 0.125 1 4 -0.54222633</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H <=2 0.5 >=16 <=0.5 -0.51743382</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C 32 2 0.5 <=0.5 -0.38692709</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J 16 1 4 1 0.04068523</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B 4 4 8 1 0.10645099</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D 32 2 2 2 0.41316947</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F 16 1 8 2 0.44073351</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I 32 1 4 2 0.45152367</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E 16 4 8 2 0.69213408</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> 1 A 8 0.025 1 1 -0.55426393</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B <=4 0.125 0.5 4 -0.42949279</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J <=4 0.25 1 1 -0.38529402</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F >=16 0.025 1 2 -0.12782528</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G <=4 0.25 4 0.5 -0.09926391</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D <=4 0.125 1 >=8 -0.05490015</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I 8 0.5 0.5 >=8 0.26246847</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H >=16 0.125 0.5 >=8 0.26899945</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E >=16 >=1 2 0.5 0.49015830</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C <=4 >=1 4 4 0.62941387</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 2 0.5 <=0.5 -0.38692709 0.0000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 H <=2 0.5 >=16 <=0.5 -0.51743382 0.1305067</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 G 4 0.125 1 4 -0.54222633 0.1552992</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 A 16 0.0625 4 <=0.5 -0.69810970 0.3111826</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 J 16 1 4 1 0.04068523 0.4276123</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 B 4 4 8 1 0.10645099 0.4933781</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 D 32 2 2 2 0.41316947 0.8000966</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 F 16 1 8 2 0.44073351 0.8276606</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I 32 1 4 2 0.45152367 0.8384508</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 E 16 4 8 2 0.69213408 1.0790612</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 >=1 4 4 0.62941387 0.0000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 E >=16 >=1 2 0.5 0.49015830 0.1392556</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 H >=16 0.125 0.5 >=8 0.26899945 0.3604144</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 I 8 0.5 0.5 >=8 0.26246847 0.3669454</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 D <=4 0.125 1 >=8 -0.05490015 0.6843140</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 G <=4 0.25 4 0.5 -0.09926391 0.7286778</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 F >=16 0.025 1 2 -0.12782528 0.7572391</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 J <=4 0.25 1 1 -0.38529402 1.0147079</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 B <=4 0.125 0.5 4 -0.42949279 1.0589067</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 A 8 0.025 1 1 -0.55426393 1.1836778</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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