mirror of
https://github.com/msberends/AMR.git
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Built site for AMR: 1.8.2.9090@51906d6
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="">1.8.2.9089</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9090</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 S I S R R R I I R</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] I S I I S I R R S R</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] -0.7745967 -0.7745967 -0.7745967 -0.7745967 1.1618950 1.1618950</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 1.1618950 -0.7745967 -0.7745967 1.1618950</span>
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<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>
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<span class="r-out co"><span class="r-pr">#></span> [8] 1.449138 -0.621059 1.449138</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] 32 2 32 0.005 0.25 0.0625 1 8 64 </span>
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<span class="r-out co"><span class="r-pr">#></span> [10] <=0.001</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 1 0.025 0.002 0.5 0.002 64 64 16 32 256 </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] 0.97437642 0.24736060 0.97437642 -1.32369446 -0.29790127 -0.66140918</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.06560664 0.61086851 1.15613038 -1.74571407</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.07454929 -0.91041921 -1.48272867 -0.23161077 -1.48272867 0.86781961</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.86781961 0.55369665 0.71075813 1.18194258</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] 0.97437642 0.24736060 0.97437642 -1.32369446 -0.29790127 -0.66140918</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.06560664 0.61086851 1.15613038 -1.74571407</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.07454929 -0.91041921 -1.48272867 -0.23161077 -1.48272867 0.86781961</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.86781961 0.55369665 0.71075813 1.18194258</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] 39 47 22 16 48 33 29 18 27 33</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 48 33 18 35 49 8 14 36 49 45</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] 0.7018456 1.4216873 -0.8278179 -1.3676991 1.5116675 0.1619644</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.1979565 -1.1877387 -0.3779169 0.1619644</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.94868330 -0.03271322 -1.01410973 0.09813965 1.01410973 -1.66837408</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -1.27581547 0.16356609 1.01410973 0.75240400</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 R 19 >=8 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B S 22 <=0.5 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C R 26 <=0.5 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D S 22 2 <=0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E S 30 4 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F R 19 >=8 16</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G R 18 2 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H S 20 2 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I R 29 <=0.5 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J R 28 <=0.5 0.5</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 19 8 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B I 20 <=2 >=4</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C I 29 <=2 >=4</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D S 23 4 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E S 29 4 >=4</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F S 30 4 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G S 19 16 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H R 17 <=2 >=4</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I R 29 16 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J S 27 8 1</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] 0.221045968 -0.709243910 -0.005209427 -0.695630697 0.480841798</span>
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<span class="r-out co"><span class="r-pr">#></span> [6] 0.804920176 0.152454865 -0.513649375 0.305692799 -0.041222197</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.61849512 -0.37440074 0.06535968 -0.22102136 0.28096952 0.12101452</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.01474925 0.07193952 0.67866446 -0.01877971</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> 10 J R 28 <=0.5 0.5 -0.98653490</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B S 22 <=0.5 1 -0.69459780</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C R 26 <=0.5 1 -0.69459780</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D S 22 2 <=0.25 -0.66737138</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I R 29 <=0.5 2 -0.40266070</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H S 20 2 1 -0.08349717</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G R 18 2 4 0.50037704</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A R 19 >=8 1 0.52760347</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E S 30 4 4 0.80592736</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F R 19 >=8 16 1.69535188</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 19 8 0.5 -0.49165184</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B I 20 <=2 >=4 -0.10118760</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C I 29 <=2 >=4 -0.10118760</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H R 17 <=2 >=4 -0.10118760</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D S 23 4 2 -0.08760245</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F S 30 4 2 -0.08760245</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J S 27 8 1 -0.07401730</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I R 29 16 0.5 -0.06043216</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E S 29 4 >=4 0.33003208</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G S 19 16 2 0.77483691</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 26 <=0.5 1 -0.005209427 0.00000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 J R 28 <=0.5 0.5 -0.041222197 0.03601277</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 G R 18 2 4 0.152454865 0.15766429</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 A R 19 >=8 1 0.221045968 0.22625539</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 I R 29 <=0.5 2 0.305692799 0.31090223</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 E S 30 4 4 0.480841798 0.48605122</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 H S 20 2 1 -0.513649375 0.50843995</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 D S 22 2 <=0.25 -0.695630697 0.69042127</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 B S 22 <=0.5 1 -0.709243910 0.70403448</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 F R 19 >=8 16 0.804920176 0.81012960</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 I 29 <=2 >=4 0.06535968 0.000000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 H R 17 <=2 >=4 0.07193952 0.006579847</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 G S 19 16 2 0.01474925 0.050610425</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 F S 30 4 2 0.12101452 0.055654841</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 J S 27 8 1 -0.01877971 0.084139390</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 E S 29 4 >=4 0.28096952 0.215609840</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 D S 23 4 2 -0.22102136 0.286381034</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 B I 20 <=2 >=4 -0.37440074 0.439760411</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I R 29 16 0.5 0.67866446 0.613304780</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 A I 19 8 0.5 -0.61849512 0.683854800</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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