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https://github.com/msberends/AMR.git
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Built site for AMR: 1.8.2.9050@7ca44fb
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="">1.8.2.9049</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9050</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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@ -200,11 +200,11 @@
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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] 2 0.01 0.01 2 0.125 <=0.005 0.0625 <=0.005 4 </span>
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<span class="r-out co"><span class="r-pr">#></span> [10] >=256 </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 2 32 128 1 0.5 0.0625 0.025 <=0.002 0.025 </span>
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<span class="r-out co"><span class="r-pr">#></span> [10] 0.25 </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] 0.6440970 -0.8222686 -0.8222686 0.6440970 -0.1232464 -1.0141044</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.3150822 -1.0141044 0.8359328 1.9869478</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.48360188 1.30293138 1.71259613 0.27876950 0.07393712 -0.54056001</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.81133368 -1.55771340 -0.81133368 -0.13089525</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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@ -214,38 +214,38 @@
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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 0.25 2 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B >=32 0.125 <=0.5 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C >=32 0.0625 <=0.5 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D 4 0.5 2 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E 8 <=0.025 2 16</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F 16 0.125 >=4 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G 4 2 <=0.5 <=1</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 0.0625 <=0.5 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J >=32 0.0625 <=0.5 4</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 1 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B 2 0.5 <=0.5 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C 8 0.5 2 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D 2 0.25 1 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E 2 0.125 <=0.5 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F 4 0.25 1 <=0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G 4 0.125 4 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 16 0.25 1 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I 4 >=1 4 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J 8 0.25 <=0.5 <=0.25</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] 0.25292590 0.13456515 -0.22939265 0.18846902 0.04421622 0.50727140</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.62066776 0.14690263 -0.19489727 -0.22939265</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.1450392 -0.4787244 0.4644919 0.0373999 -0.6166474 -0.4409559</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.1129369 0.6091625 0.8671386 -0.4097629</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> 7 G 4 2 <=0.5 <=1 -0.62066776</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C >=32 0.0625 <=0.5 4 -0.22939265</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J >=32 0.0625 <=0.5 4 -0.22939265</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I 16 0.0625 <=0.5 8 -0.19489727</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E 8 <=0.025 2 16 0.04421622</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B >=32 0.125 <=0.5 8 0.13456515</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 4 0.5 >=4 4 0.14690263</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D 4 0.5 2 8 0.18846902</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A 8 0.25 2 8 0.25292590</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F 16 0.125 >=4 8 0.50727140</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> 5 E 2 0.125 <=0.5 2 -0.6166474</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B 2 0.5 <=0.5 0.5 -0.4787244</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F 4 0.25 1 <=0.25 -0.4409559</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J 8 0.25 <=0.5 <=0.25 -0.4097629</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A 4 0.125 1 2 -0.1450392</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D 2 0.25 1 4 0.0373999</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G 4 0.125 4 1 0.1129369</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C 8 0.5 2 0.5 0.4644919</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 16 0.25 1 2 0.6091625</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I 4 >=1 4 1 0.8671386</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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@ -257,17 +257,17 @@
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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 0.0625 <=0.5 4 -0.22939265 0.00000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 J >=32 0.0625 <=0.5 4 -0.22939265 0.00000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 I 16 0.0625 <=0.5 8 -0.19489727 0.03449538</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 E 8 <=0.025 2 16 0.04421622 0.27360887</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 B >=32 0.125 <=0.5 8 0.13456515 0.36395780</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 H 4 0.5 >=4 4 0.14690263 0.37629528</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G 4 2 <=0.5 <=1 -0.62066776 0.39127511</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 D 4 0.5 2 8 0.18846902 0.41786167</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 A 8 0.25 2 8 0.25292590 0.48231854</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 F 16 0.125 >=4 8 0.50727140 0.73666405</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 0.5 2 0.5 0.4644919 0.0000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 H 16 0.25 1 2 0.6091625 0.1446706</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 G 4 0.125 4 1 0.1129369 0.3515550</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 I 4 >=1 4 1 0.8671386 0.4026467</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 D 2 0.25 1 4 0.0373999 0.4270920</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 A 4 0.125 1 2 -0.1450392 0.6095311</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 J 8 0.25 <=0.5 <=0.25 -0.4097629 0.8742548</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 F 4 0.25 1 <=0.25 -0.4409559 0.9054478</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 B 2 0.5 <=0.5 0.5 -0.4787244 0.9432163</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 E 2 0.125 <=0.5 2 -0.6166474 1.0811393</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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