mirror of
https://github.com/msberends/AMR.git
synced 2025-07-27 23:25:34 +02:00
Built site for AMR: 1.8.2.9084@86e28ba
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="">1.8.2.9083</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9084</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">
|
||||
@ -191,30 +191,31 @@
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">rsi</span> <span class="op"><-</span> <span class="fu"><a href="random.html">random_rsi</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">rsi</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'rsi'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] S R I R I R I S R I</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] R S S I S I R I S I</span>
|
||||
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">rsi</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -0.7745967 1.1618950 -0.7745967 1.1618950 -0.7745967 1.1618950</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] -0.7745967 -0.7745967 1.1618950 -0.7745967</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 1.8973666 -0.4743416 -0.4743416 -0.4743416 -0.4743416 -0.4743416</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 1.8973666 -0.4743416 -0.4743416 -0.4743416</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 0.025 128 128 0.025 0.125 32 0.01 128 0.0625</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 1 2 <=0.001 <=0.001 <=0.001 >=16 0.002 0.125 0.125 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [10] 8 </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] -0.02978237 -0.95544246 1.18775017 1.18775017 -0.95544246 -0.55158203</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 0.83988373 -1.18536967 1.18775017 -0.72551525</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.6534187 0.8306741 -1.1130696 -1.1130696 -1.1130696 1.3624400</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] -0.9358143 0.1216528 0.1216528 1.1851847</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] -0.02978237 -0.95544246 1.18775017 1.18775017 -0.95544246 -0.55158203</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 0.83988373 -1.18536967 1.18775017 -0.72551525</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.6534187 0.8306741 -1.1130696 -1.1130696 -1.1130696 1.3624400</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] -0.9358143 0.1216528 0.1216528 1.1851847</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] 45 44 9 49 49 8 6 35 47 46</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 19 41 24 49 8 47 23 25 8 21</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] 0.60645473 0.55230698 -1.34286403 0.82304570 0.82304570 -1.39701178</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] -1.50530726 0.06497729 0.71475021 0.66060247</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -0.5123570 0.9905569 -0.1707857 1.5370711 -1.2638140 1.4004425</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] -0.2390999 -0.1024714 -1.2638140 -0.3757285</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>
|
||||
@ -224,36 +225,36 @@
|
||||
<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 25 2 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 B S 19 2 >=16</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 C S 27 >=8 >=16</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 D R 21 2 >=16</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 E S 26 >=8 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 F I 21 2 >=16</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 G I 27 <=1 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 H S 25 <=1 <=1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 I I 18 <=1 8</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 J R 27 >=8 8</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 1 <=0.5</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 B I 22 >=2 >=16</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 C S 24 >=2 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 D R 26 >=2 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 E S 21 0.5 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 F R 20 0.5 <=0.5</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 G I 23 >=2 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 H I 24 1 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 I I 19 <=0.25 <=0.5</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 J S 27 <=0.25 <=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" 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] -0.3442580 -0.2743798 0.6961282 0.4613073 0.2926426 -0.1316197</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] -0.4012318 -0.7100447 -0.7115465 1.1230024</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -0.05259924 0.57930600 0.15889055 0.86335651 -0.22456313 -0.25597154</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 0.21726521 0.10735130 -1.07035142 -0.32268424</span>
|
||||
<span class="r-in"><span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span> <span class="op"><-</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span>, <span class="fu">where</span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Calculating mean AMR distance based on columns "gent" and "tobr"</span>
|
||||
<span class="r-in"><span><span class="va">y</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/order.html" class="external-link">order</a></span><span class="op">(</span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span><span class="op">)</span>, <span class="op">]</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr amr_distance</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 H S 25 <=1 <=1 -1.3827826</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 G I 27 <=1 2 -1.0506770</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 A I 25 2 2 -0.6512093</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 I I 18 <=1 8 -0.3864658</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 B S 19 2 >=16 0.3451075</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 D R 21 2 >=16 0.3451075</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 F I 21 2 >=16 0.3451075</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 E S 26 >=8 4 0.4798318</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 J R 27 >=8 8 0.8119374</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 C S 27 >=8 >=16 1.1440430</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr amr_distance</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 I I 19 <=0.25 <=0.5 -1.1572729</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 J S 27 <=0.25 <=0.5 -1.1572729</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 F R 20 0.5 <=0.5 -0.7505283</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 A R 20 1 <=0.5 -0.3437837</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 E S 21 0.5 4 0.1604701</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 H I 24 1 2 0.2635486</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 C S 24 >=2 1 0.3666271</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 D R 26 >=2 1 0.3666271</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 G I 23 >=2 2 0.6702932</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 B I 22 >=2 >=16 1.5812916</span>
|
||||
<span class="r-in"><span></span></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="va">y</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
@ -265,17 +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" 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 S 27 >=8 >=16 0.6961282 0.0000000</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 D R 21 2 >=16 0.4613073 0.2348209</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 E S 26 >=8 4 0.2926426 0.4034856</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 J R 27 >=8 8 1.1230024 0.4268743</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 F I 21 2 >=16 -0.1316197 0.8277479</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 B S 19 2 >=16 -0.2743798 0.9705080</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 A I 25 2 2 -0.3442580 1.0403862</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 G I 27 <=1 2 -0.4012318 1.0973600</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 H S 25 <=1 <=1 -0.7100447 1.4061728</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 I I 18 <=1 8 -0.7115465 1.4076747</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 24 >=2 1 0.15889055 0.00000000</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 H I 24 1 2 0.10735130 0.05153924</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 G I 23 >=2 2 0.21726521 0.05837466</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 A R 20 1 <=0.5 -0.05259924 0.21148979</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 E S 21 0.5 4 -0.22456313 0.38345368</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 F R 20 0.5 <=0.5 -0.25597154 0.41486209</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 B I 22 >=2 >=16 0.57930600 0.42041545</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 J S 27 <=0.25 <=0.5 -0.32268424 0.48157478</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 D R 26 >=2 1 0.86335651 0.70446596</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 I I 19 <=0.25 <=0.5 -1.07035142 1.22924196</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