mirror of
https://github.com/msberends/AMR.git
synced 2025-07-27 19:47:55 +02:00
Built site for AMR: 1.8.2.9060@b1ead9c
This commit is contained in:
github-actions
@ -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="">1.8.2.9059</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9060</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">
|
||||
@ -200,10 +200,11 @@
|
||||
<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>
|
||||
<span class="r-in"><span><span class="va">x</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'mic'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.125 >=2 0.005 0.01 >=2 1 0.5 0.001 0.001 0.002</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.0625 0.0625 0.5 >=32 0.025 8 0.125 >=32 0.125 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [10] <=0.005</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">#></span> [1] 0.3309983 1.2029031 -0.6812519 -0.4632756 1.2029031 0.9849269</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 0.7669507 -1.1873769 -1.1873769 -0.9694007</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -0.5687734 -0.5687734 0.1128218 1.4760124 -0.8691134 1.0216155</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] -0.3415750 1.4760124 -0.3415750 -1.3966518</span>
|
||||
<span class="r-in"><span></span></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/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>
|
||||
@ -213,38 +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">#></span> id amox cipr gent tobr</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 A 32 0.25 <=0.5 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 B 4 >=1 1 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 C 2 >=1 <=0.5 <=1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 D 8 0.5 1 <=1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 E 32 0.5 1 <=1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 F >=64 >=1 >=8 <=1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 G 1 0.25 2 <=1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 H 2 >=1 4 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 I 8 0.5 >=8 <=1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 J 32 <=0.125 1 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 A 16 2 4 <=0.5</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 B 32 1 4 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 C 32 0.0625 4 16</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 D 32 2 2 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 E 64 0.0625 4 16</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 F <=4 0.125 4 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 G 8 0.125 1 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 H 32 0.25 4 16</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 I 16 0.0625 2 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 J 32 0.25 4 1</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">#></span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> "id" and "tobr"</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>NAs introduced by coercion</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.12196526 0.40284317 -0.47762168 -0.30700434 -0.06650357 0.79277984</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] -0.73763891 0.32070406 0.19485787 -0.24438169</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.07915544 0.57522152 0.34727511 0.20664625 0.56026080 -0.71078914</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] -1.07687359 0.59727511 -0.63133944 0.05316793</span>
|
||||
<span class="r-in"><span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span> <span class="op"><-</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span>, <span class="fu">where</span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent" and</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> "tobr"</span>
|
||||
<span class="r-in"><span><span class="va">y</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/order.html" class="external-link">order</a></span><span class="op">(</span><span class="va">y</span><span class="op">$</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">#></span> id amox cipr gent tobr amr_distance</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 G 1 0.25 2 <=1 -0.73763891</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 C 2 >=1 <=0.5 <=1 -0.47762168</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 D 8 0.5 1 <=1 -0.30700434</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 J 32 <=0.125 1 2 -0.24438169</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 E 32 0.5 1 <=1 -0.06650357</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 A 32 0.25 <=0.5 4 0.12196526</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 I 8 0.5 >=8 <=1 0.19485787</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 H 2 >=1 4 2 0.32070406</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 B 4 >=1 1 4 0.40284317</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 F >=64 >=1 >=8 <=1 0.79277984</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr amr_distance</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 G 8 0.125 1 2 -1.07687359</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 F <=4 0.125 4 1 -0.71078914</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 I 16 0.0625 2 2 -0.63133944</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 J 32 0.25 4 1 0.05316793</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 A 16 2 4 <=0.5 0.07915544</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 D 32 2 2 2 0.20664625</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 C 32 0.0625 4 16 0.34727511</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 E 64 0.0625 4 16 0.56026080</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 B 32 1 4 4 0.57522152</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 H 32 0.25 4 16 0.59727511</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">%>%</a></span></span></span>
|
||||
@ -256,17 +257,17 @@
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent" and</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> "tobr"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr amr_distance check_id_C</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 C 2 >=1 <=0.5 <=1 -0.47762168 0.0000000</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 D 8 0.5 1 <=1 -0.30700434 0.1706173</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 J 32 <=0.125 1 2 -0.24438169 0.2332400</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 G 1 0.25 2 <=1 -0.73763891 0.2600172</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 E 32 0.5 1 <=1 -0.06650357 0.4111181</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 A 32 0.25 <=0.5 4 0.12196526 0.5995869</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 I 8 0.5 >=8 <=1 0.19485787 0.6724795</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 H 2 >=1 4 2 0.32070406 0.7983257</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 B 4 >=1 1 4 0.40284317 0.8804648</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 F >=64 >=1 >=8 <=1 0.79277984 1.2704015</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr amr_distance check_id_C</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 C 32 0.0625 4 16 0.34727511 0.0000000</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 D 32 2 2 2 0.20664625 0.1406289</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 E 64 0.0625 4 16 0.56026080 0.2129857</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 B 32 1 4 4 0.57522152 0.2279464</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 H 32 0.25 4 16 0.59727511 0.2500000</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 A 16 2 4 <=0.5 0.07915544 0.2681197</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 J 32 0.25 4 1 0.05316793 0.2941072</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 I 16 0.0625 2 2 -0.63133944 0.9786145</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 F <=4 0.125 4 1 -0.71078914 1.0580643</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 G 8 0.125 1 2 -1.07687359 1.4241487</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">%>%</a></span></span></span>
|
||||
|
||||
Reference in New Issue
Block a user