mirror of
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Built site for AMR: 1.8.2.9093@b94bc6c
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="">1.8.2.9092</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9093</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] S S R S R I S R I S</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] I I I R S I I I I I</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] -0.621059 -0.621059 1.449138 -0.621059 1.449138 -0.621059 -0.621059</span>
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<span class="r-out co"><span class="r-pr">#></span> [8] 1.449138 -0.621059 -0.621059</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-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] 64 0.5 <=0.025 128 4 0.0625 256 2 128 </span>
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<span class="r-out co"><span class="r-pr">#></span> [10] 0.125 </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 4 >=64 0.001 1 0.0625 0.0625 0.25 0.0625 4 4 </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] 0.84443028 -0.55224804 -1.41458279 1.04395575 0.04632838 -1.15082446</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 1.24348122 -0.15319709 1.04395575 -0.95129899</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.7050535 1.5873138 -1.9341805 0.2639234 -0.6183369 -0.6183369</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.1772067 -0.6183369 0.7050535 0.7050535</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] 0.84443028 -0.55224804 -1.41458279 1.04395575 0.04632838 -1.15082446</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 1.24348122 -0.15319709 1.04395575 -0.95129899</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.7050535 1.5873138 -1.9341805 0.2639234 -0.6183369 -0.6183369</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.1772067 -0.6183369 0.7050535 0.7050535</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] 31 19 25 45 43 45 10 42 38 47</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 38 50 21 40 26 10 16 45 24 19</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] -0.2747505 -1.2167523 -0.7457514 0.8242516 0.6672513 0.8242516</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -1.9232536 0.5887511 0.2747505 0.9812518</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.6768341 1.5693625 -0.5875812 0.8255888 -0.2156944 -1.4057323</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.9594681 1.1974757 -0.3644491 -0.7363360</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 20 <=0.25 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B R 25 1 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C I 24 0.5 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D S 17 2 >=8</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E S 25 <=0.25 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F R 28 >=4 0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G I 29 2 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H I 22 1 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I I 18 2 0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J I 21 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 I 30 8 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B S 17 4 >=4</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C R 19 8 >=4</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D R 29 2 >=4</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E I 19 8 <=1</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F R 28 8 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G R 26 8 >=4</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H I 25 1 >=4</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I R 27 4 >=4</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J R 21 0.5 <=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] -0.39633734 0.72619085 0.03532415 0.11086821 -0.37841945 0.83757068</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.41812023 -0.34726311 -0.56085146 -0.44520275</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.09446764 -0.47291812 0.29008010 0.47684186 -0.78696988 0.47223165</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.66233628 -0.39251526 0.54299934 -0.88655361</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> 5 E S 25 <=0.25 1 -0.78135160</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J I 21 0.5 1 -0.41647341</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H I 22 1 0.5 -0.34520532</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I I 18 2 0.25 -0.27393724</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A S 20 <=0.25 4 -0.19413138</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F R 28 >=4 0.25 0.09094095</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C I 24 0.5 4 0.17074681</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B R 25 1 2 0.24201490</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G I 29 2 1 0.31328298</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D S 17 2 >=8 1.19411331</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 21 0.5 <=1 -1.83069295</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E I 19 8 <=1 -0.45056183</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H I 25 1 >=4 -0.29980604</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D R 29 2 >=4 0.04522674</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A I 30 8 2 0.14236523</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F R 28 8 2 0.14236523</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B S 17 4 >=4 0.39025951</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I R 27 4 >=4 0.39025951</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C R 19 8 >=4 0.73529229</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G R 26 8 >=4 0.73529229</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 I 24 0.5 4 0.03532415 0.00000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 D S 17 2 >=8 0.11086821 0.07554406</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 H I 22 1 0.5 -0.34726311 0.38258727</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 G I 29 2 1 0.41812023 0.38279607</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E S 25 <=0.25 1 -0.37841945 0.41374361</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 A S 20 <=0.25 4 -0.39633734 0.43166149</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 J I 21 0.5 1 -0.44520275 0.48052690</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 I I 18 2 0.25 -0.56085146 0.59617562</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 B R 25 1 2 0.72619085 0.69086670</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 F R 28 >=4 0.25 0.83757068 0.80224652</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 19 8 >=4 0.29008010 0.0000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 F R 28 8 2 0.47223165 0.1821516</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 D R 29 2 >=4 0.47684186 0.1867618</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 A I 30 8 2 0.09446764 0.1956125</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 I R 27 4 >=4 0.54299934 0.2529192</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 G R 26 8 >=4 0.66233628 0.3722562</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 H I 25 1 >=4 -0.39251526 0.6825954</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 B S 17 4 >=4 -0.47291812 0.7629982</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 E I 19 8 <=1 -0.78696988 1.0770500</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J R 21 0.5 <=1 -0.88655361 1.1766337</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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