mirror of
https://github.com/msberends/AMR.git
synced 2025-07-10 01:02:47 +02:00
Built site for AMR: 2.0.0@68aa98f
This commit is contained in:
github-actions
@ -201,30 +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 R S I R S R R S R</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] I S S R S S I S R 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] 0.7745967 0.7745967 -1.1618950 -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] -0.621059 -0.621059 -0.621059 1.449138 -0.621059 -0.621059 -0.621059</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [8] -0.621059 1.449138 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] 0.002 0.002 256 0.0625 0.01 0.025 0.002 2 4 0.005 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.002 0.125 0.001 16 16 64 2 16 0.5 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] -0.867240328 -0.867240328 2.066590798 -0.008525384 -0.465717781</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [6] -0.237121583 -0.867240328 0.856106358 1.029032707 -0.638644130</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -1.45381664 -0.39257207 -1.63170516 0.85264760 0.85264760 1.20842465</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 0.31898203 0.85264760 -0.03679502 -0.57046060</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] -0.867240328 -0.867240328 2.066590798 -0.008525384 -0.465717781</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [6] -0.237121583 -0.867240328 0.856106358 1.029032707 -0.638644130</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -1.45381664 -0.39257207 -1.63170516 0.85264760 0.85264760 1.20842465</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 0.31898203 0.85264760 -0.03679502 -0.57046060</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] 42 21 42 39 44 36 46 41 9 48</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 41 7 31 43 26 15 50 45 50 36</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] 0.42276578 -1.28455756 0.42276578 0.17886245 0.58536800 -0.06504089</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 0.74797023 0.34146467 -2.26017090 0.91057245</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.4508859 -1.8718595 -0.2322745 0.5875180 -0.5738547 -1.3253312</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 1.0657302 0.7241500 1.0657302 0.1093057</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>
|
||||
@ -234,22 +234,22 @@
|
||||
<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 S 27 4 <=1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 B R 20 1 <=1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 C R 31 <=0.5 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 D S 23 4 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 E R 31 2 <=1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 F R 24 <=0.5 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 G R 28 1 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 H R 22 4 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 I S 23 8 <=1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 J S 26 4 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 R 25 >=2 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 B I 29 >=2 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 C S 30 >=2 0.5</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 D R 22 >=2 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 E R 21 1 0.25</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 F R 28 >=2 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 G R 20 1 0.5</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 H I 19 >=2 0.5</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 I S 30 1 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 J R 27 >=2 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",</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] -0.2706405 -0.6068529 0.2354050 -0.2518529 0.3034383 -0.2313769</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 0.4976524 0.4511070 -0.3605963 0.2337166</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.65477694 0.24022002 -0.02948384 0.47956157 -0.75261068 0.50188332</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] -0.64696131 -0.67194018 -0.05486954 0.27942371</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>
|
||||
@ -265,17 +265,17 @@
|
||||
<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 31 <=0.5 2 0.2354050 0.00000000</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 J S 26 4 4 0.2337166 0.00168838</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 E R 31 2 <=1 0.3034383 0.06803327</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 H R 22 4 4 0.4511070 0.21570200</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 G R 28 1 4 0.4976524 0.26224741</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 F R 24 <=0.5 2 -0.2313769 0.46678194</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 D S 23 4 2 -0.2518529 0.48725790</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 A S 27 4 <=1 -0.2706405 0.50604549</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 I S 23 8 <=1 -0.3605963 0.59600133</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 B R 20 1 <=1 -0.6068529 0.84225790</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 30 >=2 0.5 -0.02948384 0.0000000</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 I S 30 1 4 -0.05486954 0.0253857</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 B I 29 >=2 2 0.24022002 0.2697039</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 J R 27 >=2 0.5 0.27942371 0.3089076</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 D R 22 >=2 4 0.47956157 0.5090454</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 F R 28 >=2 1 0.50188332 0.5313672</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 G R 20 1 0.5 -0.64696131 0.6174775</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 H I 19 >=2 0.5 -0.67194018 0.6424563</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 A R 25 >=2 4 0.65477694 0.6842608</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 E R 21 1 0.25 -0.75261068 0.7231268</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