mirror of
https://github.com/msberends/AMR.git
synced 2025-07-09 19:01:51 +02:00
Built site for AMR: 1.8.2.9148@262598b
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="">1.8.2.9147</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9148</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">
|
||||
@ -201,30 +201,31 @@
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">sir</span> <span class="op"><-</span> <span class="fu"><a href="random.html">random_sir</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">sir</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'sir'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] S S I S R I I S S S</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] R I I I I S R S I R</span>
|
||||
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">sir</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -0.3162278 -0.3162278 -0.3162278 -0.3162278 2.8460499 -0.3162278</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] -0.3162278 -0.3162278 -0.3162278 -0.3162278</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 1.449138 -0.621059 -0.621059 -0.621059 -0.621059 -0.621059 1.449138</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [8] -0.621059 -0.621059 1.449138</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="va">mic</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">mic</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] 0.01 8 0.25 64 0.025 128 1 0.01 128 128 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.25 1 8 <=0.005 <=0.005 2 0.01 >=256 16 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [10] 8 </span>
|
||||
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">mic</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -1.3051841 0.3547377 -0.5058733 0.8711043 -1.0776509 1.0432265</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] -0.1616289 -1.3051841 1.0432265 1.0432265</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -0.27951091 0.09147782 0.64796092 -1.32641444 -1.32641444 0.27697218</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] -1.14092007 1.57543274 0.83345528 0.64796092</span>
|
||||
<span class="r-in"><span><span class="co"># equal to the Z-score of their log2:</span></span></span>
|
||||
<span class="r-in"><span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span> <span class="op">-</span> <span class="fu"><a href="https://rdrr.io/r/base/mean.html" class="external-link">mean</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span><span class="op">)</span><span class="op">)</span> <span class="op">/</span> <span class="fu"><a href="https://rdrr.io/r/stats/sd.html" class="external-link">sd</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -1.3051841 0.3547377 -0.5058733 0.8711043 -1.0776509 1.0432265</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] -0.1616289 -1.3051841 1.0432265 1.0432265</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -0.27951091 0.09147782 0.64796092 -1.32641444 -1.32641444 0.27697218</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] -1.14092007 1.57543274 0.83345528 0.64796092</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="va">disk</span> <span class="op"><-</span> <span class="fu"><a href="random.html">random_disk</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">disk</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'disk'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 17 43 40 10 41 48 32 39 42 29</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 42 21 38 40 46 49 41 15 29 48</span>
|
||||
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">disk</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -1.3988539 0.7280585 0.4826455 -1.9714842 0.5644498 1.1370801</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] -0.1717891 0.4008412 0.6462542 -0.4172021</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.44150742 -1.37646431 0.09522709 0.26836726 0.78778775 1.04749800</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 0.35493734 -1.89588481 -0.68390365 0.96092792</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>
|
||||
@ -234,22 +235,22 @@
|
||||
<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 S 17 2 >=8</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 B R 23 1 >=8</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 C I 18 8 >=8</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 D R 25 2 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 E S 30 8 >=8</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 F S 25 1 >=8</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 G I 22 0.5 >=8</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 H R 18 1 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 I S 19 4 >=8</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 J R 22 0.5 1</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 R 17 0.5 0.5</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 B I 22 4 >=8</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 C R 31 1 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 D R 23 1 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 E R 29 1 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 F I 21 1 >=8</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 G R 19 0.5 0.5</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 H S 20 0.5 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 I R 22 2 <=0.25</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 J S 19 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">#></span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> and "tobr"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -0.30902553 0.37446780 0.09125296 0.28702431 0.82880923 0.01327092</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] -0.34052588 -0.50251321 -0.01669175 -0.42606885</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -0.55862477 0.58537655 0.77602663 0.17820212 0.51539668 0.02637631</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] -0.44622659 -0.72591865 0.07694007 -0.42754836</span>
|
||||
<span class="r-in"><span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span> <span class="op"><-</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span>, <span class="fu"><a href="https://tidyselect.r-lib.org/reference/where.html" class="external-link">where</a></span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in .subset(x, j):</span> invalid subscript type 'list'</span>
|
||||
<span class="r-in"><span><span class="va">y</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/order.html" class="external-link">order</a></span><span class="op">(</span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span><span class="op">)</span>, <span class="op">]</span></span></span>
|
||||
@ -265,17 +266,17 @@
|
||||
<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",</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> and "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 I 18 8 >=8 0.09125296 0.00000000</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 F S 25 1 >=8 0.01327092 0.07798204</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 I S 19 4 >=8 -0.01669175 0.10794471</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 D R 25 2 2 0.28702431 0.19577135</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 B R 23 1 >=8 0.37446780 0.28321484</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 A S 17 2 >=8 -0.30902553 0.40027849</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 G I 22 0.5 >=8 -0.34052588 0.43177884</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 J R 22 0.5 1 -0.42606885 0.51732181</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 H R 18 1 1 -0.50251321 0.59376617</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 E S 30 8 >=8 0.82880923 0.73755627</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 R 31 1 2 0.77602663 0.0000000</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 B I 22 4 >=8 0.58537655 0.1906501</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 E R 29 1 1 0.51539668 0.2606300</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 D R 23 1 1 0.17820212 0.5978245</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 I R 22 2 <=0.25 0.07694007 0.6990866</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 F I 21 1 >=8 0.02637631 0.7496503</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 J S 19 2 0.5 -0.42754836 1.2035750</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 G R 19 0.5 0.5 -0.44622659 1.2222532</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 A R 17 0.5 0.5 -0.55862477 1.3346514</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 H S 20 0.5 1 -0.72591865 1.5019453</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