mirror of
https://github.com/msberends/AMR.git
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Built site for AMR: 1.8.2.9086@84ed8c3
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="">1.8.2.9085</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9086</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 I I I S S R S S R</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] S R R R I I I 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] -0.4743416 -0.4743416 -0.4743416 -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 1.8973666</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.9486833 0.9486833 0.9486833 0.9486833 -0.9486833 -0.9486833</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.9486833 0.9486833 -0.9486833 0.9486833</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 4 0.005 <=0.002 8 0.125 16 64 >=256 </span>
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<span class="r-out co"><span class="r-pr">#></span> [10] 0.025 </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 2 0.025 >=128 0.025 >=128 16 4 >=128 8 0.025</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] 0.7759961 0.2799572 -1.3146188 -1.5331947 0.4453035 -0.5467743</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.6106498 0.9413425 1.2720351 -0.9306965</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.09761619 -1.32347254 1.06581655 -1.32347254 1.06581655 0.48410018</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.09628927 1.06581655 0.29019472 -1.32347254</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] 0.7759961 0.2799572 -1.3146188 -1.5331947 0.4453035 -0.5467743</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.6106498 0.9413425 1.2720351 -0.9306965</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.09761619 -1.32347254 1.06581655 -1.32347254 1.06581655 0.48410018</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.09628927 1.06581655 0.29019472 -1.32347254</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] 34 40 49 17 45 36 20 20 48 18</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 44 29 31 8 26 23 36 34 41 46</span>
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<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">disk</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.1006272 0.5650602 1.2617097 -1.2152664 0.9520877 0.2554382</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.9830499 -0.9830499 1.1843042 -1.1378609</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 1.0822909 -0.2483946 -0.0709699 -2.1113544 -0.5145317 -0.7806689</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.3725920 0.1951672 0.8161538 1.2597157</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 I 19 <=0.25 <=0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B R 21 0.5 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C I 30 1 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D S 30 8 >=4</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E R 18 <=0.25 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F I 29 16 >=4</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G S 24 4 <=0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H I 21 4 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I I 28 2 >=4</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J S 26 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 27 0.5 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B I 27 2 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C S 20 >=8 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D I 27 4 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E I 22 4 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F S 31 2 <=1</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G S 26 1 >=16</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H R 21 4 <=1</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I R 31 4 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J S 30 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">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] -1.0443988 0.1699505 0.1816530 0.7332860 -0.1102573 0.7972126</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.3020597 -0.2666282 0.3891516 -0.5479098</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.50096961 -0.27264058 0.11352599 -0.05965490 -0.17279077 -0.22166036</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.04514514 -0.03730406 0.78189474 0.32445439</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> 1 A I 19 <=0.25 <=0.5 -1.24603939</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J S 26 0.5 <=0.5 -1.01004560</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E R 18 <=0.25 2 -0.45546997</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G S 24 4 <=0.5 -0.30206422</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B R 21 0.5 2 -0.21947618</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C I 30 1 2 0.01651761</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H I 21 4 1 0.09322048</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I I 28 2 >=4 0.64779611</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D S 30 8 >=4 1.11978369</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F I 29 16 >=4 1.35577748</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 27 0.5 4 -0.8642174</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F S 31 2 <=1 -0.8028441</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B I 27 2 2 -0.4075594</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H R 21 4 <=1 -0.3768727</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D I 27 4 2 0.0184120</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I R 31 4 2 0.0184120</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G S 26 1 >=16 0.3523234</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E I 22 4 4 0.4136967</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J S 30 4 4 0.4136967</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C S 20 >=8 8 1.2349528</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 30 1 2 0.1816530 0.00000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B R 21 0.5 2 0.1699505 0.01170248</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 I I 28 2 >=4 0.3891516 0.20749866</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 E R 18 <=0.25 2 -0.1102573 0.29191026</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 H I 21 4 1 -0.2666282 0.44828121</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 G S 24 4 <=0.5 -0.3020597 0.48371268</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 D S 30 8 >=4 0.7332860 0.55163304</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 F I 29 16 >=4 0.7972126 0.61555964</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 J S 26 0.5 <=0.5 -0.5479098 0.72956278</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 A I 19 <=0.25 <=0.5 -1.0443988 1.22605173</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 20 >=8 8 0.11352599 0.00000000</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> 2 G S 26 1 >=16 0.04514514 0.06838084</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> 3 H R 21 4 <=1 -0.03730406 0.15083004</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D I 27 4 2 -0.05965490 0.17318088</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> 5 J S 30 4 4 0.32445439 0.21092841</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 E I 22 4 4 -0.17279077 0.28631675</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 F S 31 2 <=1 -0.22166036 0.33518634</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> 8 B I 27 2 2 -0.27264058 0.38616657</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> 9 A I 27 0.5 4 -0.50096961 0.61449559</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 I R 31 4 2 0.78189474 0.66836876</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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