mirror of
https://github.com/msberends/AMR.git
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Built site for AMR: 1.8.2.9079@51c0f08
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="">1.8.2.9078</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9079</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 S R S S S I R</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] S I R S I I R I S 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] -0.4743416 -0.4743416 -0.4743416 -0.4743416 1.8973666 -0.4743416</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.4743416 -0.4743416 -0.4743416 1.8973666</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.4743416 -0.4743416 1.8973666 -0.4743416 -0.4743416 -0.4743416</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 1.8973666 -0.4743416 -0.4743416 -0.4743416</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 0.25 16 0.001 0.125 32 0.125 0.001 0.002 8 </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.025 0.25 <=0.002 0.0625 0.005 >=256 0.25 0.01 0.01 </span>
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<span class="r-out co"><span class="r-pr">#></span> [10] 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">mic</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 1.26281480 -0.01764874 0.94269891 -1.29263579 -0.17770669 1.10275686</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.17770669 -1.29263579 -1.13257785 0.78264097</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.36458316 0.30826076 -1.10263240 -0.09683165 -0.83488088 2.33372278</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.30826076 -0.63233468 -0.63233468 0.71335316</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] 1.26281480 -0.01764874 0.94269891 -1.29263579 -0.17770669 1.10275686</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.17770669 -1.29263579 -1.13257785 0.78264097</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.36458316 0.30826076 -1.10263240 -0.09683165 -0.83488088 2.33372278</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.30826076 -0.63233468 -0.63233468 0.71335316</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] 17 29 32 37 48 40 28 37 40 49</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 12 41 32 36 28 23 7 49 36 37</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] -1.9401430 -0.6951315 -0.3838786 0.1348763 1.2761369 0.4461291</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.7988824 0.1348763 0.4461291 1.3798878</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -1.3960299 0.8407031 0.1465446 0.4550595 -0.1619703 -0.5476139</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -1.7816735 1.4577329 0.4550595 0.5321882</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 R 23 >=16 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B I 24 1 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C S 24 8 0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D R 18 2 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E S 17 4 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F S 22 8 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G R 29 2 0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H S 28 >=16 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I I 31 4 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J S 20 >=16 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 R 20 <=0.5 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B S 19 16 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C R 25 8 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D R 30 2 >=8</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E R 28 1 >=8</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F I 26 <=0.5 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G I 21 1 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H S 22 1 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I S 25 2 >=8</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J S 18 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] 0.76502575 -0.22559420 -0.39112580 0.14405101 -0.59747772 0.01884049</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.04569124 0.34391737 0.15560237 -0.25893050</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.25809138 -0.09594429 0.26834683 1.00209109 0.73552766 -0.19144637</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.53806425 -0.65193856 0.20590130 -0.47638203</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> 7 G R 29 2 0.25 -1.2141339</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C S 24 8 0.25 -0.5147553</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B I 24 1 4 -0.1836920</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E S 17 4 1 -0.1743790</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I I 31 4 1 -0.1743790</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D R 18 2 4 0.1659973</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J S 20 >=16 0.5 0.1799668</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F S 22 8 2 0.5203431</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H S 28 >=16 1 0.5249996</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A R 23 >=16 2 0.8700324</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> 8 H S 22 1 1 -0.7418213</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A R 20 <=0.5 2 -0.6727193</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G I 21 1 2 -0.3892460</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F I 26 <=0.5 4 -0.3201439</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C R 25 8 0.5 -0.2439766</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J S 18 8 1 0.1085987</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E R 28 1 >=8 0.3159048</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D R 30 2 >=8 0.5993781</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I S 25 2 >=8 0.5993781</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B S 19 16 2 0.7446475</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 S 24 8 0.25 -0.39112580 0.0000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 J S 20 >=16 0.5 -0.25893050 0.1321953</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 B I 24 1 4 -0.22559420 0.1655316</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 E S 17 4 1 -0.59747772 0.2063519</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 F S 22 8 2 0.01884049 0.4099663</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 G R 29 2 0.25 0.04569124 0.4368170</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 D R 18 2 4 0.14405101 0.5351768</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 I I 31 4 1 0.15560237 0.5467282</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 H S 28 >=16 1 0.34391737 0.7350432</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 A R 23 >=16 2 0.76502575 1.1561516</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 25 8 0.5 0.26834683 0.00000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 I S 25 2 >=8 0.20590130 0.06244553</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 B S 19 16 2 -0.09594429 0.36429112</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 F I 26 <=0.5 4 -0.19144637 0.45979320</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E R 28 1 >=8 0.73552766 0.46718083</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 A R 20 <=0.5 2 -0.25809138 0.52643821</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> 7 D R 30 2 >=8 1.00209109 0.73374426</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 J S 18 8 1 -0.47638203 0.74472886</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 G I 21 1 2 -0.53806425 0.80641108</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 H S 22 1 1 -0.65193856 0.92028539</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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