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https://github.com/msberends/AMR.git
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Built site for AMR: 1.8.2.9103@126afb0
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="">1.8.2.9102</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9103</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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@ -196,30 +196,31 @@
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<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">sir</span> <span class="op"><-</span> <span class="fu"><a href="random.html">random_sir</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">sir</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> Class 'sir'</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] I R S S I I R R S S</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] S I R I S R R I R S</span>
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<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">sir</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.621059 1.449138 -0.621059 -0.621059 -0.621059 -0.621059 1.449138</span>
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<span class="r-out co"><span class="r-pr">#></span> [8] 1.449138 -0.621059 -0.621059</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.7745967 -0.7745967 1.1618950 -0.7745967 -0.7745967 1.1618950</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 1.1618950 -0.7745967 1.1618950 -0.7745967</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 0.025 0.25 1 0.125 0.0625 32 >=128 0.002 0.01 </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.5 0.005 4 0.005 4 16 8 >=128 <=0.002</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-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] 1.2951529 -0.7433996 -0.1452749 0.2148320 -0.3253284 -0.5053819</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 1.1150994 1.4752064 -1.3994886 -0.9814174</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.004555148 -1.189296722 0.543632982 -1.189296722 0.543632982</span>
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<span class="r-out co"><span class="r-pr">#></span> [6] 0.903018205 0.723325594 1.442096040 -1.426837433 -0.354830075</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] 1.2951529 -0.7433996 -0.1452749 0.2148320 -0.3253284 -0.5053819</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 1.1150994 1.4752064 -1.3994886 -0.9814174</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.004555148 -1.189296722 0.543632982 -1.189296722 0.543632982</span>
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<span class="r-out co"><span class="r-pr">#></span> [6] 0.903018205 0.723325594 1.442096040 -1.426837433 -0.354830075</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] 23 33 39 43 50 20 48 32 20 37</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 8 32 43 15 44 37 16 14 29 29</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] -1.0485886 -0.1367724 0.4103173 0.7750438 1.4133151 -1.3221335</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 1.2309519 -0.2279540 -1.3221335 0.2279540</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -1.4621577 0.4144083 1.2745011 -0.9148259 1.3526913 0.8053596</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.8366357 -0.9930162 0.1798376 0.1798376</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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@ -229,36 +230,36 @@
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<span class="r-in"><span> tobr <span class="op">=</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span>, ab <span class="op">=</span> <span class="st">"tobr"</span>, mo <span class="op">=</span> <span class="st">"Escherichia coli"</span><span class="op">)</span></span></span>
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<span class="r-in"><span><span class="op">)</span></span></span>
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<span class="r-in"><span><span class="va">y</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A R 19 8 <=0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B I 20 16 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C S 21 2 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D R 30 4 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E I 22 2 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F S 28 16 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G S 31 1 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H R 21 4 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I R 21 8 <=0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J I 20 16 2</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 25 16 0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B I 30 16 0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C I 28 0.5 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D I 26 16 0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E S 26 8 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F R 21 16 0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G S 19 2 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H I 27 8 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I R 19 8 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J R 28 8 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] -0.26006002 -0.13428531 -0.41365492 0.93268272 -0.54826784 0.49780904</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.22563105 0.24531265 -0.14950859 0.05560332</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.19598774 0.12451337 -0.09209741 -0.13188752 -0.14956959 0.06516053</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.63363528 0.05123363 0.05598101 0.90628900</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 S 31 1 1 -0.9152098</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A R 19 8 <=0.25 -0.6256964</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I R 21 8 <=0.25 -0.6256964</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E I 22 2 1 -0.5655205</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C S 21 2 2 -0.1857432</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H R 21 4 2 0.1639461</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B I 20 16 1 0.4835474</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D R 30 4 4 0.5437234</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F S 28 16 2 0.8633247</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J I 20 16 2 0.8633247</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> 3 C I 28 0.5 8 -0.27108669</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G S 19 2 2 -0.20035843</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E S 26 8 0.5 -0.12963016</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A I 25 16 0.25 -0.09426603</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B I 30 16 0.25 -0.09426603</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D I 26 16 0.25 -0.09426603</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F R 21 16 0.25 -0.09426603</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H I 27 8 1 0.14377582</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I R 19 8 1 0.14377582</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J R 28 8 4 0.69058778</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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@ -270,17 +271,17 @@
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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 21 2 2 -0.41365492 0.0000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 E I 22 2 1 -0.54826784 0.1346129</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 A R 19 8 <=0.25 -0.26006002 0.1535949</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 G S 31 1 1 -0.22563105 0.1880239</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 I R 21 8 <=0.25 -0.14950859 0.2641463</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 B I 20 16 1 -0.13428531 0.2793696</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 J I 20 16 2 0.05560332 0.4692582</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H R 21 4 2 0.24531265 0.6589676</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 F S 28 16 2 0.49780904 0.9114640</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 D R 30 4 4 0.93268272 1.3463376</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 28 0.5 8 -0.09209741 0.00000000</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> 2 D I 26 16 0.25 -0.13188752 0.03979011</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 E S 26 8 0.5 -0.14956959 0.05747218</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> 4 A I 25 16 0.25 -0.19598774 0.10389034</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 H I 27 8 1 0.05123363 0.14333103</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> 6 I R 19 8 1 0.05598101 0.14807842</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 F R 21 16 0.25 0.06516053 0.15725794</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 B I 30 16 0.25 0.12451337 0.21661078</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> 9 G S 19 2 2 -0.63363528 0.54153787</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J R 28 8 4 0.90628900 0.99838641</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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