P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-27 19:47:55 +02:00
Code Releases Activity

Built site for AMR: 1.8.2.9062@8da2467

Browse Source
This commit is contained in:
github-actions
2022-12-11 23:23:03 +00:00
parent 7b50c6e9f7
commit 64384886d7
101 changed files with 4953 additions and 842 deletions
Download Patch File Download Diff File Expand all files Collapse all files

80
reference/mean_amr_distance.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9061</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9062</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -200,11 +200,11 @@
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">x</span> <span class="op">&lt;-</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>
<span class="r-in"><span><span class="va">x</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 16 0.25 8 0.025 128 4 0.0625 0.0625 &lt;=0.002</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 0.025 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.125 4 0.025 32 &lt;=0.001 128 0.002 16 &lt;=0.001</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 1 </span>
<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>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1.0547374 -0.1257265 0.8579935 -0.7792959 1.6449694 0.6612495</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.5192145 -0.5192145 -1.4962027 -0.7792959</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.1673708 0.6088797 -0.5278503 1.0746300 -1.2488094 1.3851301</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -1.0935593 0.9193799 -1.2488094 0.2983795</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">y</span> <span class="op">&lt;-</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>
<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>
@ -214,38 +214,38 @@
<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>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">y</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A 16 0.5 4 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B &gt;=32 0.5 1 8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C 4 0.25 2 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D 16 0.5 4 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 8 &gt;=1 4 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F 2 0.125 4 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G 1 0.5 &gt;=8 0.5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H 2 &gt;=1 4 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I 16 &gt;=1 &gt;=8 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J 16 0.125 4 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A &gt;=64 4 1 0.5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B 4 1 &gt;=4 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C 16 &lt;=0.125 &gt;=4 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D 8 2 2 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 32 1 1 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F 8 0.25 &gt;=4 0.5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G &gt;=64 0.5 2 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H 4 0.5 &gt;=4 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I &gt;=64 2 1 0.5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J 16 &lt;=0.125 2 0.5</span>
<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>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> "id" and "tobr"</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>NAs introduced by coercion</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.036743946 0.196829201 -0.376851467 0.425339766 0.497315583</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [6] -0.848366515 -0.464960905 0.006554142 0.542471648 -0.015075399</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.12023536 0.33318132 0.20872945 0.16343985 -0.14151184 -0.36277928</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.52860021 -0.18662082 -0.02573319 -0.63754106</span>
<span class="r-in"><span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span> <span class="op">&lt;-</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span>, <span class="fu">where</span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent" and</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> "tobr"</span>
<span class="r-in"><span><span class="va">y</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/order.html" class="external-link">order</a></span><span class="op">(</span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span><span class="op">)</span>, <span class="op">]</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr amr_distance</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F 2 0.125 4 1 -0.848366515</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G 1 0.5 &gt;=8 0.5 -0.464960905</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C 4 0.25 2 4 -0.376851467</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J 16 0.125 4 4 -0.015075399</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H 2 &gt;=1 4 2 0.006554142</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A 16 0.5 4 1 0.036743946</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B &gt;=32 0.5 1 8 0.196829201</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D 16 0.5 4 4 0.425339766</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 8 &gt;=1 4 4 0.497315583</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I 16 &gt;=1 &gt;=8 1 0.542471648</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr amr_distance</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J 16 &lt;=0.125 2 0.5 -0.63754106</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F 8 0.25 &gt;=4 0.5 -0.36277928</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H 4 0.5 &gt;=4 1 -0.18662082</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 32 1 1 1 -0.14151184</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I &gt;=64 2 1 0.5 -0.02573319</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A &gt;=64 4 1 0.5 0.12023536</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D 8 2 2 2 0.16343985</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C 16 &lt;=0.125 &gt;=4 4 0.20872945</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B 4 1 &gt;=4 4 0.33318132</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G &gt;=64 0.5 2 4 0.52860021</span>
<span class="r-in"><span></span></span>
<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>
<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">%&gt;%</a></span></span></span>
@ -257,17 +257,17 @@
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent" and</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> "tobr"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr amr_distance check_id_C</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 C 4 0.25 2 4 -0.376851467 0.00000000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 G 1 0.5 &gt;=8 0.5 -0.464960905 0.08810944</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 J 16 0.125 4 4 -0.015075399 0.36177607</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 H 2 &gt;=1 4 2 0.006554142 0.38340561</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 A 16 0.5 4 1 0.036743946 0.41359541</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F 2 0.125 4 1 -0.848366515 0.47151505</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 B &gt;=32 0.5 1 8 0.196829201 0.57368067</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 D 16 0.5 4 4 0.425339766 0.80219123</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 E 8 &gt;=1 4 4 0.497315583 0.87416705</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 I 16 &gt;=1 &gt;=8 1 0.542471648 0.91932312</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr amr_distance check_id_C</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 C 16 &lt;=0.125 &gt;=4 4 0.20872945 0.00000000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 D 8 2 2 2 0.16343985 0.04528960</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 A &gt;=64 4 1 0.5 0.12023536 0.08849408</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 B 4 1 &gt;=4 4 0.33318132 0.12445187</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 I &gt;=64 2 1 0.5 -0.02573319 0.23446263</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 G &gt;=64 0.5 2 4 0.52860021 0.31987077</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 E 32 1 1 1 -0.14151184 0.35024128</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H 4 0.5 &gt;=4 1 -0.18662082 0.39535027</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 F 8 0.25 &gt;=4 0.5 -0.36277928 0.57150872</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J 16 &lt;=0.125 2 0.5 -0.63754106 0.84627050</span>
<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>
<span class="r-in"><span> <span class="co"># support for groups</span></span></span>
<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">%&gt;%</a></span></span></span>