mirror of
https://github.com/msberends/AMR.git
synced 2025-07-27 17:07:54 +02:00
Built site for AMR: 2.0.0.9024@f065945
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="">2.0.0.9023</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9024</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">
|
||||
@ -218,30 +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 R R I S I I S S</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] I R I I R R R I R 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] -0.4743416 -0.4743416 1.8973666 1.8973666 -0.4743416 -0.4743416</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] -0.4743416 -0.4743416 -0.4743416 -0.4743416</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -0.9486833 0.9486833 -0.9486833 -0.9486833 0.9486833 0.9486833</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 0.9486833 -0.9486833 0.9486833 -0.9486833</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] 8 >=16 0.002 >=16 0.025 >=16 0.002 2 2 2 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 256 0.01 4 64 8 1 1 0.002 0.125 256 </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] 0.6738475 0.8649910 -1.6133339 0.8649910 -0.9168346 0.8649910</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] -1.6133339 0.2915606 0.2915606 0.2915606</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 1.2331707 -1.2886091 0.1999266 0.8887560 0.3721339 -0.1444882</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] -0.1444882 -1.6884622 -0.6611102 1.2331707</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] 0.6738475 0.8649910 -1.6133339 0.8649910 -0.9168346 0.8649910</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] -1.6133339 0.2915606 0.2915606 0.2915606</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 1.2331707 -1.2886091 0.1999266 0.8887560 0.3721339 -0.1444882</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] -0.1444882 -1.6884622 -0.6611102 1.2331707</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] 39 15 22 38 19 50 29 46 40 18</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 25 6 45 23 39 45 20 49 8 43</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] 0.5869812 -1.3167417 -0.7614892 0.5076595 -0.9994545 1.4595209</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] -0.2062367 1.1422338 0.6663030 -1.0787763</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -0.3319640 -1.5220235 0.9207303 -0.4572334 0.5449220 0.9207303</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] -0.6451375 1.1712691 -1.3967541 0.7954608</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>
|
||||
@ -251,22 +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 I 17 8 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 B S 31 2 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 C R 19 16 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 D S 18 8 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 E S 19 16 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 F I 31 16 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 G I 24 <=1 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 H S 24 <=1 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 I R 22 4 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 J R 20 2 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 27 1 0.5</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 B R 29 1 0.5</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 C I 19 <=0.5 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 D I 27 1 <=0.25</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 E S 30 <=0.5 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 F I 22 1 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 G I 26 1 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 H R 22 1 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 I I 21 4 0.5</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 J R 29 1 <=0.25</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] -0.06628516 0.31654289 0.46727798 -0.49122694 -0.05027119 0.77969806</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] -0.42081207 -0.65798290 0.54387830 -0.42081897</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.27087972 0.39969323 -0.52646026 -0.38265093 0.18201405 -0.36586924</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] -0.10824222 0.28766141 0.01268871 0.23028550</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>
|
||||
@ -282,17 +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 R 19 16 2 0.46727798 0.00000000</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 I R 22 4 4 0.54387830 0.07660032</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 B S 31 2 4 0.31654289 0.15073509</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 F I 31 16 4 0.77969806 0.31242008</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 E S 19 16 2 -0.05027119 0.51754917</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 A I 17 8 4 -0.06628516 0.53356314</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 G I 24 <=1 2 -0.42081207 0.88809005</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 J R 20 2 0.5 -0.42081897 0.88809695</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 D S 18 8 1 -0.49122694 0.95850492</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 H S 24 <=1 1 -0.65798290 1.12526088</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 19 <=0.5 4 -0.52646026 0.0000000</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 D I 27 1 <=0.25 -0.38265093 0.1438093</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 F I 22 1 1 -0.36586924 0.1605910</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 G I 26 1 1 -0.10824222 0.4182180</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 I I 21 4 0.5 0.01268871 0.5391490</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 E S 30 <=0.5 4 0.18201405 0.7084743</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 J R 29 1 <=0.25 0.23028550 0.7567458</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 A R 27 1 0.5 0.27087972 0.7973400</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 H R 22 1 2 0.28766141 0.8141217</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 B R 29 1 0.5 0.39969323 0.9261535</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