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https://github.com/msberends/AMR.git
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Built site for AMR: 1.8.2.9081@268ec31
This commit is contained in:
github-actions
@ -10,7 +10,7 @@
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9080</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9081</small>
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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@ -191,31 +191,30 @@
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<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>
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<span class="r-in"><span><span class="va">rsi</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> Class 'rsi'</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] I R I I S I S I I I</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] S S R I I R R R I S</span>
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<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>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.3162278 2.8460499 -0.3162278 -0.3162278 -0.3162278 -0.3162278</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.3162278 -0.3162278 -0.3162278 -0.3162278</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.7745967 -0.7745967 1.1618950 -0.7745967 -0.7745967 1.1618950</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 1.1618950 1.1618950 -0.7745967 -0.7745967</span>
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<span class="r-in"><span></span></span>
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<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>
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<span class="r-in"><span><span class="va">mic</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> Class 'mic'</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 256 <=0.001 0.005 0.5 0.25 4 32 128 64 </span>
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<span class="r-out co"><span class="r-pr">#></span> [10] 256 </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 32 0.001 >=64 0.01 0.001 2 0.002 0.005 0.002 0.125</span>
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<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>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.99293867 -1.76809231 -1.41125204 -0.39020601 -0.54388875 0.07084222</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.53189044 0.83925593 0.68557318 0.99293867</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 1.5006685 -0.9103327 1.6617694 -0.3751671 -0.9103327 0.8562649</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.7492318 -0.5362680 -0.7492318 0.2118614</span>
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<span class="r-in"><span><span class="co"># equal to the Z-score of their log2:</span></span></span>
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<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>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.99293867 -1.76809231 -1.41125204 -0.39020601 -0.54388875 0.07084222</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.53189044 0.83925593 0.68557318 0.99293867</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 1.5006685 -0.9103327 1.6617694 -0.3751671 -0.9103327 0.8562649</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.7492318 -0.5362680 -0.7492318 0.2118614</span>
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<span class="r-in"><span></span></span>
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<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>
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<span class="r-in"><span><span class="va">disk</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> Class 'disk'</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 19 33 22 41 43 10 7 15 48 7</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 50 50 42 10 25 25 24 41 14 46</span>
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<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>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.3527042 0.5450884 -0.1603201 1.0581127 1.1863688 -0.9298566</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -1.1222407 -0.6092164 1.5070090 -1.1222407</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 1.1634023 1.1634023 0.6254128 -1.5265452 -0.5178149 -0.5178149</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.5850636 0.5581641 -1.2575504 0.8944075</span>
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<span class="r-in"><span></span></span>
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<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>
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<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>
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@ -225,36 +224,36 @@
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<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>
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<span class="r-in"><span><span class="op">)</span></span></span>
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<span class="r-in"><span><span class="va">y</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A S 24 8 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B S 29 2 <=0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C R 21 16 >=4</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D R 28 8 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E I 24 4 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F R 27 16 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G S 18 8 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H R 30 8 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I R 18 <=0.5 <=0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J S 21 <=0.5 <=0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A I 28 1 <=1</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B S 18 2 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C S 26 >=8 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D R 28 >=8 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E I 31 2 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F R 23 1 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G R 23 4 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H I 31 4 <=1</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I I 18 >=8 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J I 17 2 2</span>
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<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>
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<span class="r-msg co"><span class="r-pr">#></span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent" and</span>
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<span class="r-msg co"><span class="r-pr">#></span> "tobr"</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.0285555 -0.3644751 0.7598507 0.4975482 -0.3378487 0.9246795</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.5421272 0.9593579 -0.7818441 -1.0865856</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.7306638 -0.4034429 0.3974553 1.0087361 0.2058131 0.1354498</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.5614212 -0.1640949 -0.1717694 -0.8389046</span>
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<span class="r-in"><span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span> <span class="op"><-</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span>, <span class="fu">where</span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span><span class="op">)</span></span></span>
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<span class="r-msg co"><span class="r-pr">#></span> ℹ Calculating mean AMR distance based on columns "gent" and "tobr"</span>
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<span class="r-in"><span><span class="va">y</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/order.html" class="external-link">order</a></span><span class="op">(</span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span><span class="op">)</span>, <span class="op">]</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr amr_distance</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I R 18 <=0.5 <=0.25 -1.35962934</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J S 21 <=0.5 <=0.25 -1.35962934</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B S 29 2 <=0.25 -0.81994226</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E I 24 4 0.5 -0.20135581</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D R 28 8 0.5 0.06848772</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G S 18 8 0.5 0.06848772</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A S 24 8 1 0.41723064</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H R 30 8 2 0.76597356</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F R 27 16 2 1.03581709</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C R 21 16 >=4 1.38456001</span>
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<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr amr_distance</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A I 28 1 <=1 -1.49760542</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J I 17 2 2 -0.68303823</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H I 31 4 <=1 -0.64566267</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F R 23 1 8 -0.33181796</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B S 18 2 8 0.09415341</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E I 31 2 8 0.09415341</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G R 23 4 8 0.52012479</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I I 18 >=8 4 0.55750034</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C S 26 >=8 8 0.94609616</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D R 28 >=8 8 0.94609616</span>
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<span class="r-in"><span></span></span>
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<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>
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<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>
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@ -266,17 +265,17 @@
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<span class="r-in"><span><span class="op">}</span></span></span>
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<span class="r-msg co"><span class="r-pr">#></span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent" and</span>
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<span class="r-msg co"><span class="r-pr">#></span> "tobr"</span>
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<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr amr_distance check_id_C</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 C R 21 16 >=4 0.7598507 0.0000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 F R 27 16 2 0.9246795 0.1648288</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 H R 30 8 2 0.9593579 0.1995072</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D R 28 8 0.5 0.4975482 0.2623025</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 A S 24 8 1 -0.0285555 0.7884062</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 E I 24 4 0.5 -0.3378487 1.0976994</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 B S 29 2 <=0.25 -0.3644751 1.1243258</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 G S 18 8 0.5 -0.5421272 1.3019779</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I R 18 <=0.5 <=0.25 -0.7818441 1.5416948</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J S 21 <=0.5 <=0.25 -1.0865856 1.8464363</span>
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<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr amr_distance check_id_C</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 C S 26 >=8 8 0.3974553 0.0000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 G R 23 4 8 0.5614212 0.1639659</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 E I 31 2 8 0.2058131 0.1916421</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 F R 23 1 8 0.1354498 0.2620054</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 H I 31 4 <=1 -0.1640949 0.5615502</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 I I 18 >=8 4 -0.1717694 0.5692247</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> 7 D R 28 >=8 8 1.0087361 0.6112809</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 B S 18 2 8 -0.4034429 0.8008982</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> 9 A I 28 1 <=1 -0.7306638 1.1281191</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J I 17 2 2 -0.8389046 1.2363598</span>
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<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>
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<span class="r-in"><span> <span class="co"># support for groups</span></span></span>
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<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>
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