mirror of
https://github.com/msberends/AMR.git
synced 2025-07-27 17:07:54 +02:00
Built site for AMR: 2.0.0.9008@ad3061c
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="">2.0.0.9007</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9008</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">
|
||||
@ -201,31 +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] I R S S S R R I R I</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] R R R R S R R I I I</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] -0.7745967 1.1618950 -0.7745967 -0.7745967 -0.7745967 1.1618950</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 1.1618950 -0.7745967 1.1618950 -0.7745967</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.7745967 0.7745967 0.7745967 0.7745967 -1.1618950 0.7745967</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 0.7745967 -1.1618950 -1.1618950 -1.1618950</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] <=0.001 0.025 32 0.01 0.0625 0.125 0.5 0.01 8 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] <=0.005 0.125 0.025 0.01 0.25 0.5 >=128 2 0.25 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [10] 2 </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] -1.5257422 -0.5427941 1.6420106 -0.8226018 -0.2629864 -0.0513201</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 0.3720126 -0.8226018 1.2186779 0.7953453</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -1.34952811 -0.26581181 -0.80766996 -1.11616251 -0.03244621 0.20091939</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 2.06784421 0.66765060 -0.03244621 0.66765060</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] -1.5257422 -0.5427941 1.6420106 -0.8226018 -0.2629864 -0.0513201</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 0.3720126 -0.8226018 1.2186779 0.7953453</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -1.34952811 -0.26581181 -0.80766996 -1.11616251 -0.03244621 0.20091939</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 2.06784421 0.66765060 -0.03244621 0.66765060</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] 16 44 41 26 44 46 48 50 48 40</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 18 34 13 40 31 21 44 32 40 41</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] -2.23059935 0.33963858 0.06425595 -1.31265723 0.33963858 0.52322701</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 0.70681543 0.89040385 0.70681543 -0.02753826</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -1.25112890 0.24275635 -1.71796804 0.80296332 -0.03734713 -0.97102541</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 1.17643463 0.05602070 0.80296332 0.89633115</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>
|
||||
@ -235,22 +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 I 21 >=4 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 B R 28 2 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 C S 23 >=4 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 D I 20 1 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 E I 27 1 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 F S 20 2 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 G I 25 >=4 <=0.5</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 H S 25 2 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 I R 20 1 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 J R 22 >=4 <=0.5</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 18 <=0.5 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 B I 23 2 16</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 C R 19 2 <=1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 D I 24 4 <=1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 E R 23 8 16</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 F R 27 8 16</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 G R 21 1 16</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 H S 18 16 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 I S 21 <=0.5 16</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 J I 20 1 4</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] 0.37458457 0.92678423 0.01430793 -0.80688677 -0.22319302 -0.25784351</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] -0.08244556 0.15908059 -0.28933760 0.18494914</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -0.56956384 0.09857482 -0.33782767 -0.23465405 0.85843659 1.20624076</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 0.25625432 -0.33010519 -0.36084739 -0.58650835</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>
|
||||
@ -266,17 +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 S 23 >=4 1 0.01430793 0.0000000</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 G I 25 >=4 <=0.5 -0.08244556 0.0967535</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 H S 25 2 2 0.15908059 0.1447727</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 J R 22 >=4 <=0.5 0.18494914 0.1706412</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 E I 27 1 1 -0.22319302 0.2375010</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 F S 20 2 2 -0.25784351 0.2721514</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 I R 20 1 1 -0.28933760 0.3036455</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 A I 21 >=4 4 0.37458457 0.3602766</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 D I 20 1 1 -0.80688677 0.8211947</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 B R 28 2 2 0.92678423 0.9124763</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 19 2 <=1 -0.33782767 0.000000000</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 H S 18 16 2 -0.33010519 0.007722481</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 I S 21 <=0.5 16 -0.36084739 0.023019715</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 D I 24 4 <=1 -0.23465405 0.103173626</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 A R 18 <=0.5 2 -0.56956384 0.231736171</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 J I 20 1 4 -0.58650835 0.248680682</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 B I 23 2 16 0.09857482 0.436402492</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 G R 21 1 16 0.25625432 0.594081995</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 E R 23 8 16 0.85843659 1.196264261</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 F R 27 8 16 1.20624076 1.544068433</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