mirror of
https://github.com/msberends/AMR.git
synced 2025-07-27 17:07:54 +02:00
Built site for AMR: 2.0.0.9022@e196650
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="">2.0.0.9021</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9022</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">
|
||||
@ -218,31 +218,30 @@
|
||||
<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] I I S R I R S R I I</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] S R S I I I R S R S</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] -0.621059 -0.621059 -0.621059 1.449138 -0.621059 1.449138 -0.621059</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [8] 1.449138 -0.621059 -0.621059</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -0.621059 1.449138 -0.621059 -0.621059 -0.621059 -0.621059 1.449138</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [8] -0.621059 1.449138 -0.621059</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] 0.5 >=256 0.01 128 2 0.0625 0.25 >=256 <=0.005</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [10] 8 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.5 4 1 0.001 32 0.125 0.25 0.125 0.125 64 </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] -0.2688902 1.2713130 -1.2347441 1.1001793 0.0733772 -0.7822912</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] -0.4400238 1.2713130 -1.4058777 0.4156446</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -0.02261165 0.63329547 0.19602406 -1.98285222 1.28920259 -0.45988306</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] -0.24124735 -0.45988306 -0.45988306 1.50783829</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] -0.2688902 1.2713130 -1.2347441 1.1001793 0.0733772 -0.7822912</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] -0.4400238 1.2713130 -1.4058777 0.4156446</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -0.02261165 0.63329547 0.19602406 -1.98285222 1.28920259 -0.45988306</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] -0.24124735 -0.45988306 -0.45988306 1.50783829</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] 48 34 46 9 17 8 45 43 48 23</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 12 39 10 7 40 39 30 44 18 39</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] 0.9710659 0.1160393 0.8489193 -1.4107939 -0.9222073 -1.4718672</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 0.7878459 0.6656993 0.9710659 -0.5557673</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -1.0909965 0.7733646 -1.2290973 -1.4362486 0.8424150 0.7733646</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 0.1519109 1.1186167 -0.6766940 0.7733646</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>
|
||||
@ -252,22 +251,22 @@
|
||||
<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 21 1 <=0.25</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 B R 22 8 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 C I 30 1 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 D S 19 2 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 E S 28 4 16</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 F I 27 1 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 G I 29 4 8</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 H I 27 8 <=0.25</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 I R 19 4 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 J S 25 4 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 S 27 1 0.5</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 B I 28 2 >=4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 C S 28 >=4 >=4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 D S 18 >=4 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 E S 19 >=4 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 F S 30 >=4 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 G I 28 1 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 H S 26 2 >=4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 I R 21 >=4 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 J R 18 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] -1.05388613 0.61671804 -0.12926825 -0.45476979 0.55502550 -0.18356494</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 0.48848798 -0.05498737 0.35028931 -0.13404436</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -0.7116852 0.2836947 0.5873608 -0.3661781 -0.1004357 0.2669030</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] -0.2329571 0.1781812 0.3850192 -0.2899029</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>
|
||||
@ -283,17 +282,17 @@
|
||||
<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 30 1 2 -0.12926825 0.000000000</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 J S 25 4 1 -0.13404436 0.004776111</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 F I 27 1 4 -0.18356494 0.054296697</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 H I 27 8 <=0.25 -0.05498737 0.074280879</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 D S 19 2 4 -0.45476979 0.325501539</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 I R 19 4 4 0.35028931 0.479557557</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 G I 29 4 8 0.48848798 0.617756223</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 E S 28 4 16 0.55502550 0.684293745</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 B R 22 8 2 0.61671804 0.745986288</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 A S 21 1 <=0.25 -1.05388613 0.924617881</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 S 28 >=4 >=4 0.5873608 0.0000000</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 I R 21 >=4 1 0.3850192 0.2023416</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 B I 28 2 >=4 0.2836947 0.3036661</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 F S 30 >=4 1 0.2669030 0.3204579</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 H S 26 2 >=4 0.1781812 0.4091796</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 E S 19 >=4 2 -0.1004357 0.6877965</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 G I 28 1 2 -0.2329571 0.8203179</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 J R 18 2 0.5 -0.2899029 0.8772637</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 D S 18 >=4 1 -0.3661781 0.9535390</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 A S 27 1 0.5 -0.7116852 1.2990461</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