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https://github.com/msberends/AMR.git
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Built site for AMR: 1.8.2.9040@796b972
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="">1.8.2.9039</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9040</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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@ -195,10 +195,11 @@
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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] 0.125 128 0.5 0.001 0.002 32 0.01 0.0625 0.0625 0.01 </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 32 128 <=0.001 0.125 0.025 16 0.01 16 64 </span>
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<span class="r-out co"><span class="r-pr">#></span> [10] 0.01 </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] 0.03977575 1.83205678 0.39823196 -1.20868855 -1.02946045 1.47360058</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.61330568 -0.13945235 -0.13945235 -0.61330568</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.8741078 1.1886741 -1.4797580 -0.3841574 -0.7493576 0.7168247</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.9572746 0.7168247 1.0313910 -0.9572746</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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@ -208,38 +209,38 @@
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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 1 <=0.5 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B 32 0.025 <=0.5 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C <=2 0.5 2 <=1</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D 64 >=2 1 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E 16 0.25 4 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F 4 0.25 <=0.5 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G 32 0.125 1 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 16 0.25 <=0.5 <=1</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I 64 >=2 8 <=1</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J 64 1 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 2 0.5 2 >=4</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B 16 1 >=4 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C 8 >=2 2 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D 1 0.25 2 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E 1 1 >=4 >=4</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F 1 0.25 2 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G 2 1 >=4 >=4</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 8 0.5 2 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I 4 >=2 >=4 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J 16 0.25 2 >=4</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] -0.1805861 -0.3593922 -0.5470696 0.4524955 0.1519544 -0.3106839</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.1028200 -0.6317241 0.6651338 0.6570522</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.1488052 0.6945257 0.2690034 -1.1500416 0.3939183 -0.8331088</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.5483034 -0.4739008 0.5987413 0.1013643</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> 8 H 16 0.25 <=0.5 <=1 -0.6317241</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C <=2 0.5 2 <=1 -0.5470696</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B 32 0.025 <=0.5 4 -0.3593922</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F 4 0.25 <=0.5 4 -0.3106839</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A <=2 1 <=0.5 4 -0.1805861</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G 32 0.125 1 4 0.1028200</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E 16 0.25 4 2 0.1519544</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D 64 >=2 1 2 0.4524955</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J 64 1 4 2 0.6570522</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I 64 >=2 8 <=1 0.6651338</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 1 0.25 2 1 -1.1500416</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F 1 0.25 2 2 -0.8331088</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 8 0.5 2 1 -0.4739008</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A 2 0.5 2 >=4 -0.1488052</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J 16 0.25 2 >=4 0.1013643</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C 8 >=2 2 2 0.2690034</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E 1 1 >=4 >=4 0.3939183</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G 2 1 >=4 >=4 0.5483034</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I 4 >=2 >=4 2 0.5987413</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B 16 1 >=4 2 0.6945257</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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@ -251,17 +252,17 @@
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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 <=2 0.5 2 <=1 -0.5470696 0.0000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 H 16 0.25 <=0.5 <=1 -0.6317241 0.0846545</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 B 32 0.025 <=0.5 4 -0.3593922 0.1876774</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 F 4 0.25 <=0.5 4 -0.3106839 0.2363857</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 A <=2 1 <=0.5 4 -0.1805861 0.3664836</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 G 32 0.125 1 4 0.1028200 0.6498896</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 E 16 0.25 4 2 0.1519544 0.6990240</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 D 64 >=2 1 2 0.4524955 0.9995652</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 J 64 1 4 2 0.6570522 1.2041218</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 I 64 >=2 8 <=1 0.6651338 1.2122034</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 2 0.2690034 0.0000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 E 1 1 >=4 >=4 0.3939183 0.1249149</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 J 16 0.25 2 >=4 0.1013643 0.1676392</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 G 2 1 >=4 >=4 0.5483034 0.2793000</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 I 4 >=2 >=4 2 0.5987413 0.3297379</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 A 2 0.5 2 >=4 -0.1488052 0.4178086</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 B 16 1 >=4 2 0.6945257 0.4255223</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 8 0.5 2 1 -0.4739008 0.7429042</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 F 1 0.25 2 2 -0.8331088 1.1021122</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 D 1 0.25 2 1 -1.1500416 1.4190451</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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