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https://github.com/msberends/AMR.git
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Built site for AMR: 1.8.2.9115@03294c7
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="">1.8.2.9114</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9115</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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@ -201,30 +201,31 @@
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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] R I R I S R R S R I</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] S S S R R R S R R 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">sir</span><span class="op">)</span></span></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-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] 0.25 256 0.025 0.002 0.001 0.5 2 4 0.005 8 </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.025 0.01 32 0.01 <=0.005 2 0.125 8 1 </span>
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<span class="r-out co"><span class="r-pr">#></span> [10] <=0.005</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] 0.01539492 1.73098732 -0.55451254 -1.17964974 -1.35120898 0.18695416</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.53007264 0.70163188 -0.95286076 0.87319112</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.53764948 -0.81832873 1.65396061 -0.81832873 -1.03065438 0.80465801</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.04464459 1.22930931 0.59233236 -1.03065438</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] 0.01539492 1.73098732 -0.55451254 -1.17964974 -1.35120898 0.18695416</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.53007264 0.70163188 -0.95286076 0.87319112</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.53764948 -0.81832873 1.65396061 -0.81832873 -1.03065438 0.80465801</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.04464459 1.22930931 0.59233236 -1.03065438</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 25 19 19 27 30 18 38 50 41</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 28 46 25 46 31 40 19 25 41 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] 0.366179696 -0.478850372 -1.042203750 -1.042203750 -0.291065912</span>
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<span class="r-out co"><span class="r-pr">#></span> [6] -0.009389223 -1.136095980 0.741748615 1.868455372 1.023425304</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.38138504 1.33484762 -0.66742381 1.33484762 -0.09534626 0.76277007</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -1.23950137 -0.66742381 0.85811633 -1.23950137</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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@ -234,22 +235,22 @@
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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 17 >=4 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B S 18 0.5 <=1</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C R 28 1 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D S 19 2 16</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E S 30 0.5 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F R 28 <=0.25 <=1</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G S 19 1 <=1</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H S 25 >=4 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I I 19 2 16</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J I 22 2 <=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 4 0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B I 17 4 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C R 21 4 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D S 24 4 0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E R 24 1 >=8</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F R 17 1 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G I 24 1 >=8</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H R 23 8 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I R 31 4 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J R 19 2 0.25</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] 0.47149064 -0.85816127 0.51476172 0.17345726 -0.08631742 -0.01059476</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.61955106 0.51901166 0.17345726 -0.27755402</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.03691267 -0.21295353 0.22918196 -0.34893153 0.29506113 -0.56896087</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.18906179 0.44075337 0.74921339 -0.35738946</span>
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<span class="r-in"><span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span> <span class="op"><-</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span>, <span class="fu"><a href="https://tidyselect.r-lib.org/reference/where.html" class="external-link">where</a></span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span><span class="op">)</span></span></span>
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<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in .subset(x, j):</span> invalid subscript type 'list'</span>
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<span class="r-in"><span><span class="va">y</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/order.html" class="external-link">order</a></span><span class="op">(</span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span><span class="op">)</span>, <span class="op">]</span></span></span>
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@ -265,17 +266,17 @@
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<span class="r-in"><span><span class="op">}</span></span></span>
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<span class="r-msg co"><span class="r-pr">#></span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent" and</span>
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<span class="r-msg co"><span class="r-pr">#></span> "tobr"</span>
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<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr amr_distance check_id_C</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 C R 28 1 2 0.51476172 0.000000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 H S 25 >=4 8 0.51901166 0.004249942</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 A R 17 >=4 4 0.47149064 0.043271080</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D S 19 2 16 0.17345726 0.341304453</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 I I 19 2 16 0.17345726 0.341304453</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F R 28 <=0.25 <=1 -0.01059476 0.525356471</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 E S 30 0.5 2 -0.08631742 0.601079137</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 J I 22 2 <=1 -0.27755402 0.792315739</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 G S 19 1 <=1 -0.61955106 1.134312775</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 B S 18 0.5 <=1 -0.85816127 1.372922984</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 21 4 1 0.22918196 0.00000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 E R 24 1 >=8 0.29506113 0.06587918</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 H R 23 8 0.5 0.44075337 0.21157141</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 A I 30 4 0.25 -0.03691267 0.26609463</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 G I 24 1 >=8 -0.18906179 0.41824374</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 B I 17 4 4 -0.21295353 0.44213549</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 I R 31 4 1 0.74921339 0.52003143</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 D S 24 4 0.25 -0.34893153 0.57811349</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 J R 19 2 0.25 -0.35738946 0.58657141</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 F R 17 1 0.5 -0.56896087 0.79814283</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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