mirror of
https://github.com/msberends/AMR.git
synced 2025-07-27 17:07:54 +02:00
Built site for AMR@2.1.1.9133: 9520977
This commit is contained in:
github-actions
@ -7,7 +7,7 @@
|
||||
|
||||
<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="">2.1.1.9125</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9133</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">
|
||||
@ -109,30 +109,31 @@
|
||||
<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 I S I I S S S R R</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] S I S I I I R R 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] -0.4743416 -0.4743416 -0.4743416 -0.4743416 -0.4743416 -0.4743416</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] -0.4743416 -0.4743416 1.8973666 1.8973666</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -0.621059 -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 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] 0.001 256 0.25 0.5 32 0.002 8 0.125 0.002 0.125</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 64 16 8 64 256 0.5 128 128 2 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [10] <=0.002</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] -1.2863106 1.6478483 0.0146555 0.1779748 1.1578905 -1.1229914</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 0.8312519 -0.1486638 -1.1229914 -0.1486638</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.54295251 0.15465479 -0.03949407 0.54295251 0.93125022 -0.81608950</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 0.73710137 0.73710137 -0.42779178 -2.36263742</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] -1.2863106 1.6478483 0.0146555 0.1779748 1.1578905 -1.1229914</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 0.8312519 -0.1486638 -1.1229914 -0.1486638</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.54295251 0.15465479 -0.03949407 0.54295251 0.93125022 -0.81608950</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 0.73710137 0.73710137 -0.42779178 -2.36263742</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] 41 29 40 12 16 7 45 46 22 9</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 28 27 30 48 9 45 12 26 42 25</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] 0.9256143 0.1488750 0.8608860 -0.9515056 -0.6925925 -1.2751469</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 1.1845274 1.2492556 -0.3042229 -1.1456904</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -0.09277857 -0.17009405 0.06185238 1.45353101 -1.56177268 1.22158457</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] -1.32982624 -0.24740953 0.98963813 -0.32472501</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>
|
||||
@ -142,22 +143,22 @@
|
||||
<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 R 29 <=1 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 B I 30 4 <=2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 C I 26 16 16</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 D I 18 2 8</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 E S 29 4 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 F R 31 16 <=2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 G S 31 <=1 16</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 H R 21 16 16</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 I I 31 16 16</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 J S 21 <=1 4</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 28 2 0.5</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 B R 29 1 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 C S 23 4 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 D I 27 4 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 E S 19 1 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 F S 22 0.5 <=0.25</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 G I 26 1 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 H R 17 2 0.5</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 I S 19 1 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 J I 30 2 2</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] 0.04629994 -0.34117383 0.33391321 -0.69063550 -0.19222473 0.50618460</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 0.02978803 0.59753857 0.58783703 -0.87752733</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -0.06537260 0.82078512 0.42232605 0.47166071 -0.31061057 -1.07205573</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 0.06631747 -0.06476102 -0.64271615 0.37442671</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>
|
||||
@ -173,17 +174,17 @@
|
||||
<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 26 16 16 0.33391321 0.0000000</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 F R 31 16 <=2 0.50618460 0.1722714</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 I I 31 16 16 0.58783703 0.2539238</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 H R 21 16 16 0.59753857 0.2636254</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 A R 29 <=1 4 0.04629994 0.2876133</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 G S 31 <=1 16 0.02978803 0.3041252</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 E S 29 4 4 -0.19222473 0.5261379</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 B I 30 4 <=2 -0.34117383 0.6750870</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 D I 18 2 8 -0.69063550 1.0245487</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 J S 21 <=1 4 -0.87752733 1.2114405</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 4 0.42232605 0.00000000</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 J I 30 2 2 0.37442671 0.04789934</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 D I 27 4 2 0.47166071 0.04933466</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 G I 26 1 4 0.06631747 0.35600858</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 B R 29 1 4 0.82078512 0.39845906</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 H R 17 2 0.5 -0.06476102 0.48708707</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 A I 28 2 0.5 -0.06537260 0.48769865</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 E S 19 1 4 -0.31061057 0.73293662</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 I S 19 1 1 -0.64271615 1.06504220</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 F S 22 0.5 <=0.25 -1.07205573 1.49438178</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