P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-27 17:07:54 +02:00
Code Releases Activity

Built site for AMR: 1.8.2.9047@d2edcf5

Browse Source
This commit is contained in:
github-actions
2022-11-12 11:17:17 +00:00
parent 68a0b3f94a
commit 6fd5ff2a24
36 changed files with 486 additions and 485 deletions
Download Patch File Download Diff File Expand all files Collapse all files

78
reference/mean_amr_distance.html
View File

@ -195,11 +195,11 @@
<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] 0.0625 32 128 0.01 0.125 8 256 &lt;=0.002 0.005 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 32 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1 0.005 2 0.125 0.002 0.5 0.0625 0.5 &lt;=0.001</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 0.002 </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] -0.5813297 0.8047503 1.1127681 -0.9885071 -0.4273208 0.4967325</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 1.2667770 -1.3461046 -1.1425160 0.8047503</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1.04271494 -0.78781830 1.28219266 0.32428178 -1.10439062 0.80323722</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.08480407 0.80323722 -1.34386834 -1.10439062</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>
@ -209,38 +209,38 @@
<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 &lt;=4 1 8 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B 16 0.5 4 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C 8 0.5 1 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D 16 &lt;=0.125 2 &lt;=0.5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E &lt;=4 0.25 2 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F 8 1 1 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G 16 &lt;=0.125 4 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H 8 &gt;=2 2 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I &gt;=32 &gt;=2 &gt;=16 &lt;=0.5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J &lt;=4 &gt;=2 4 1</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 4 0.5 &lt;=1 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B 8 &gt;=1 2 &gt;=16</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C &gt;=16 0.5 2 0.5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D &gt;=16 0.25 2 &gt;=16</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 8 0.25 2 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F 4 0.25 4 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G &gt;=16 0.5 2 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H 4 0.25 2 &gt;=16</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I 4 0.5 4 8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J 8 0.025 4 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] -0.029889016 0.523024563 -0.540292979 -0.632651576 -0.531264758</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [6] 0.045216758 -0.009037847 0.402397473 0.840490389 -0.067993008</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.54407797 0.54766468 0.06869358 0.48271367 -0.27421097 -0.16444638</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.18654471 -0.08832657 0.36434257 -0.57889732</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> 4 D 16 &lt;=0.125 2 &lt;=0.5 -0.632651576</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C 8 0.5 1 1 -0.540292979</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E &lt;=4 0.25 2 2 -0.531264758</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J &lt;=4 &gt;=2 4 1 -0.067993008</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A &lt;=4 1 8 1 -0.029889016</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G 16 &lt;=0.125 4 2 -0.009037847</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F 8 1 1 4 0.045216758</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H 8 &gt;=2 2 4 0.402397473</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B 16 0.5 4 4 0.523024563</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I &gt;=32 &gt;=2 &gt;=16 &lt;=0.5 0.840490389</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 8 0.025 4 0.5 -0.57889732</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A 4 0.5 &lt;=1 4 -0.54407797</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 8 0.25 2 1 -0.27421097</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F 4 0.25 4 1 -0.16444638</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H 4 0.25 2 &gt;=16 -0.08832657</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C &gt;=16 0.5 2 0.5 0.06869358</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G &gt;=16 0.5 2 1 0.18654471</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I 4 0.5 4 8 0.36434257</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D &gt;=16 0.25 2 &gt;=16 0.48271367</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B 8 &gt;=1 2 &gt;=16 0.54766468</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>
@ -252,17 +252,17 @@
<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 8 0.5 1 1 -0.540292979 0.000000000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 E &lt;=4 0.25 2 2 -0.531264758 0.009028221</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 D 16 &lt;=0.125 2 &lt;=0.5 -0.632651576 0.092358597</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 J &lt;=4 &gt;=2 4 1 -0.067993008 0.472299971</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 A &lt;=4 1 8 1 -0.029889016 0.510403963</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 G 16 &lt;=0.125 4 2 -0.009037847 0.531255132</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 F 8 1 1 4 0.045216758 0.585509737</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H 8 &gt;=2 2 4 0.402397473 0.942690452</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 B 16 0.5 4 4 0.523024563 1.063317542</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 I &gt;=32 &gt;=2 &gt;=16 &lt;=0.5 0.840490389 1.380783368</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 &gt;=16 0.5 2 0.5 0.06869358 0.0000000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 G &gt;=16 0.5 2 1 0.18654471 0.1178511</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 H 4 0.25 2 &gt;=16 -0.08832657 0.1570202</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 F 4 0.25 4 1 -0.16444638 0.2331400</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 I 4 0.5 4 8 0.36434257 0.2956490</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 E 8 0.25 2 1 -0.27421097 0.3429046</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 D &gt;=16 0.25 2 &gt;=16 0.48271367 0.4140201</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 B 8 &gt;=1 2 &gt;=16 0.54766468 0.4789711</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 A 4 0.5 &lt;=1 4 -0.54407797 0.6127716</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J 8 0.025 4 0.5 -0.57889732 0.6475909</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>