mirror of
https://github.com/msberends/AMR.git
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Built site for AMR: 1.8.2.9089@1029aa2
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="">1.8.2.9088</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9089</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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@ -191,30 +191,31 @@
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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] S I S R S I S S S S</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-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 -0.3162278 -0.3162278 2.8460499 -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 -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-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] 0.005 32 >=64 0.001 32 0.005 >=64 0.001 >=64 32 </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-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] -0.9977554 0.7020018 0.8364352 -1.3099002 0.7020018 -0.9977554</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.8364352 -1.3099002 0.8364352 0.7020018</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-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] -0.9977554 0.7020018 0.8364352 -1.3099002 0.7020018 -0.9977554</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.8364352 -1.3099002 0.8364352 0.7020018</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-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] 43 13 6 50 43 19 14 23 8 44</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-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] 0.9878564 -0.7867359 -1.2008074 1.4019279 0.9878564 -0.4318175</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.7275828 -0.1952051 -1.0825013 1.0470094</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-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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@ -224,36 +225,36 @@
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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 I 22 4 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B I 24 0.5 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C R 30 2 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D S 29 0.5 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E I 30 4 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F R 19 0.25 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G I 26 4 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H S 22 2 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I S 29 2 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J I 28 0.5 1</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-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] -0.03769893 -0.40858317 0.58133901 -0.40733070 0.47139759 0.01703862</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.53378217 -0.20375172 -0.07522511 -0.47096776</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-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> 4 D S 29 0.5 1 -0.97204037</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J I 28 0.5 1 -0.97204037</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B I 24 0.5 2 -0.33817468</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C R 30 2 1 -0.30782920</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I S 29 2 1 -0.30782920</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F R 19 0.25 4 -0.03641457</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H S 22 2 2 0.32603649</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A I 22 4 2 0.65814207</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E I 30 4 2 0.65814207</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G I 26 4 4 1.29200776</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-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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@ -265,17 +266,17 @@
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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 30 2 1 0.58133901 0.00000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 G I 26 4 4 0.53378217 0.04755684</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 E I 30 4 2 0.47139759 0.10994142</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 F R 19 0.25 4 0.01703862 0.56430040</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 A I 22 4 2 -0.03769893 0.61903794</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 I S 29 2 1 -0.07522511 0.65656413</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 H S 22 2 2 -0.20375172 0.78509073</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 D S 29 0.5 1 -0.40733070 0.98866971</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 B I 24 0.5 2 -0.40858317 0.98992219</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J I 28 0.5 1 -0.47096776 1.05230677</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-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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