mirror of
https://github.com/msberends/AMR.git
synced 2025-07-11 12:22:01 +02:00
Built site for AMR: 1.8.2.9135@8dcf101
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="">1.8.2.9133</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9135</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 +201,30 @@
|
||||
<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] R I I S I I R R S I</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] S R I I R I I I 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] 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] 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 1.449138 -0.621059 -0.621059</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] 1 0.005 2 128 0.125 4 64 0.005 <=0.002</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [10] 0.5 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 32 32 0.125 4 4 >=64 2 0.5 0.005 0.0625</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] 0.2188173 -1.1461872 0.3973926 1.4688449 -0.3169088 0.5759680</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 1.2902695 -1.1461872 -1.3822510 0.0402419</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 1.0079457 1.0079457 -0.7982526 0.3306214 0.3306214 1.2337205</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 0.1048466 -0.3467030 -1.8467183 -1.0240274</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] 0.2188173 -1.1461872 0.3973926 1.4688449 -0.3169088 0.5759680</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 1.2902695 -1.1461872 -1.3822510 0.0402419</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 1.0079457 1.0079457 -0.7982526 0.3306214 0.3306214 1.2337205</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 0.1048466 -0.3467030 -1.8467183 -1.0240274</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] 10 33 46 15 27 48 6 15 12 44</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 49 50 20 39 10 28 36 49 30 15</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] -0.96532813 0.45791206 1.26235218 -0.65592809 0.08663201 1.38611219</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] -1.21284817 -0.65592809 -0.84156812 1.13859216</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 1.1286066 1.1974241 -0.8671002 0.4404319 -1.5552750 -0.3165604</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 0.2339794 1.1286066 -0.1789254 -1.2111876</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>
|
||||
@ -236,21 +235,21 @@
|
||||
<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 R 20 0.5 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 B I 28 <=0.25 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 C R 20 1 0.25</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 D R 29 8 0.5</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 E I 18 8 0.5</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 F S 26 4 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 G S 31 2 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 H S 23 <=0.25 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 I I 18 1 0.25</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 J S 20 <=0.25 0.5</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 A R 22 8 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 B I 30 8 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 C R 17 1 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 D S 21 8 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 E I 30 4 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 F S 26 1 >=8</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 G R 30 <=0.25 <=1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 H S 19 <=0.25 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 I I 20 >=16 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 J S 30 8 <=1</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" and</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> "tobr"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.29766161 -0.07440712 -0.14767835 0.83786596 -0.24885180 0.46766889</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 0.60068160 -0.19036005 -0.76871271 -0.77386803</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.64107458 0.50414230 -0.20653344 -0.19610529 0.11953242 0.24821858</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] -0.08519718 -0.85404097 -0.13112611 -0.03996489</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>
|
||||
@ -267,16 +266,16 @@
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent" and</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> "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 20 1 0.25 -0.14767835 0.00000000</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 H S 23 <=0.25 4 -0.19036005 0.04268170</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 B I 28 <=0.25 2 -0.07440712 0.07327123</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 E I 18 8 0.5 -0.24885180 0.10117345</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 A R 20 0.5 4 0.29766161 0.44533996</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 F S 26 4 4 0.46766889 0.61534723</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 I I 18 1 0.25 -0.76871271 0.62103437</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 J S 20 <=0.25 0.5 -0.77386803 0.62618968</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 G S 31 2 4 0.60068160 0.74835994</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 D R 29 8 0.5 0.83786596 0.98554431</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 C R 17 1 2 -0.20653344 0.00000000</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 D S 21 8 2 -0.19610529 0.01042815</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 I I 20 >=16 2 -0.13112611 0.07540733</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 G R 30 <=0.25 <=1 -0.08519718 0.12133626</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 J S 30 8 <=1 -0.03996489 0.16656856</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 E I 30 4 2 0.11953242 0.32606586</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 F S 26 1 >=8 0.24821858 0.45475202</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 H S 19 <=0.25 2 -0.85404097 0.64750753</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 B I 30 8 4 0.50414230 0.71067574</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 A R 22 8 4 0.64107458 0.84760803</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