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Built site for AMR: 1.8.2.9006@b9342d1
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="">1.8.2.9004</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9006</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 +195,10 @@
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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] 0.25 256 16 0.001 8 8 0.002 8 0.0625 16 </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.01 0.005 32 0.0625 64 8 32 128 32 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">x</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.3351460 1.3348700 0.6668636 -1.6654448 0.4998620 0.4998620</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -1.4984432 0.4998620 -0.6691492 0.6668636</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -1.4413339 -1.6234335 0.6790078 -0.9598887 0.8611074 0.3148086</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.6790078 1.0432070 0.6790078 -0.2314903</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 +208,38 @@
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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 4 2 1 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B 8 2 1 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C 4 0.25 >=4 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D <=1 0.125 0.5 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E <=1 0.5 2 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F <=1 0.25 >=4 <=0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G 4 >=4 2 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 4 0.25 >=4 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I 8 1 2 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J 4 0.5 2 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 8 <=0.125 >=4 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B 32 1 >=4 >=8</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C 16 <=0.125 0.5 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D 2 1 >=4 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E 16 2 2 >=8</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F 32 1 1 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G 8 <=0.125 2 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 64 0.5 >=4 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I <=1 1 <=0.25 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J 8 1 <=0.25 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] 0.40198724 0.61497293 0.04169761 -1.42617241 -0.07813388 -0.65411731</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.53631944 0.17661937 0.17391127 0.21291573</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.2588266 1.0285049 -0.4029969 -0.2130881 0.9050097 0.2023447</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.4103494 0.3029914 -0.7808350 -0.3727546</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> 4 D <=1 0.125 0.5 0.5 -1.42617241</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F <=1 0.25 >=4 <=0.25 -0.65411731</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E <=1 0.5 2 8 -0.07813388</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C 4 0.25 >=4 1 0.04169761</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I 8 1 2 0.5 0.17391127</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 4 0.25 >=4 2 0.17661937</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J 4 0.5 2 4 0.21291573</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A 4 2 1 8 0.40198724</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G 4 >=4 2 2 0.53631944</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B 8 2 1 8 0.61497293</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 <=1 1 <=0.25 1 -0.7808350</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G 8 <=0.125 2 1 -0.4103494</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C 16 <=0.125 0.5 2 -0.4029969</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J 8 1 <=0.25 1 -0.3727546</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A 8 <=0.125 >=4 1 -0.2588266</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D 2 1 >=4 0.5 -0.2130881</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F 32 1 1 1 0.2023447</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 64 0.5 >=4 0.5 0.3029914</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E 16 2 2 >=8 0.9050097</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B 32 1 >=4 >=8 1.0285049</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 +251,17 @@
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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 4 0.25 >=4 1 0.04169761 0.0000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 E <=1 0.5 2 8 -0.07813388 0.1198315</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 I 8 1 2 0.5 0.17391127 0.1322137</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 H 4 0.25 >=4 2 0.17661937 0.1349218</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 J 4 0.5 2 4 0.21291573 0.1712181</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 A 4 2 1 8 0.40198724 0.3602896</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G 4 >=4 2 2 0.53631944 0.4946218</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 B 8 2 1 8 0.61497293 0.5732753</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 F <=1 0.25 >=4 <=0.25 -0.65411731 0.6958149</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 D <=1 0.125 0.5 0.5 -1.42617241 1.4678700</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 <=0.125 0.5 2 -0.4029969 0.000000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 G 8 <=0.125 2 1 -0.4103494 0.007352492</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 J 8 1 <=0.25 1 -0.3727546 0.030242332</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 A 8 <=0.125 >=4 1 -0.2588266 0.144170390</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 D 2 1 >=4 0.5 -0.2130881 0.189908807</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 I <=1 1 <=0.25 1 -0.7808350 0.377838058</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 F 32 1 1 1 0.2023447 0.605341690</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 64 0.5 >=4 0.5 0.3029914 0.705988302</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 E 16 2 2 >=8 0.9050097 1.308006638</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 B 32 1 >=4 >=8 1.0285049 1.431501827</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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