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https://github.com/msberends/AMR.git
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Built site for AMR: 1.8.2.9125@8d37c75
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="">1.8.2.9124</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9125</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 +201,30 @@
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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] S R S R R I I I R R</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] I S S I R S S 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">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] -0.621059 -0.621059 -0.621059 -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 1.449138</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 2 0.001 2 0.025 256 0.025 64 0.025 0.5 </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.001 4 1 64 0.01 4 0.025 0.002 0.5 >=128</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] -0.12797444 0.41517764 -1.57018523 0.41517764 -0.72941183 1.68253251</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.72941183 1.32043112 -0.72941183 0.05307625</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -1.41273419 0.58164698 0.24829965 1.24834166 -0.85905624 0.58164698</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.63872564 -1.24606052 0.08162598 1.41501533</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] -0.12797444 0.41517764 -1.57018523 0.41517764 -0.72941183 1.68253251</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.72941183 1.32043112 -0.72941183 0.05307625</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -1.41273419 0.58164698 0.24829965 1.24834166 -0.85905624 0.58164698</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.63872564 -1.24606052 0.08162598 1.41501533</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] 22 47 8 19 40 38 47 19 7 8</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 40 31 10 19 43 48 7 32 9 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] -0.2169449 1.3326617 -1.0847246 -0.4028977 0.8987718 0.7748033</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 1.3326617 -0.4028977 -1.1467089 -1.0847246</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.8882407 0.2826221 -1.1304882 -0.5248695 1.0901136 1.4265685</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -1.3323611 0.3499130 -1.1977792 0.1480401</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 +234,22 @@
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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 S 26 1 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B S 20 0.25 16</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C I 23 8 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D R 30 4 16</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E R 31 0.25 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F R 23 8 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G R 31 16 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H R 26 0.25 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I R 20 0.25 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J I 17 1 <=0.25</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 26 1 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B S 21 0.5 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C I 20 1 16</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D S 23 0.25 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E R 25 1 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F I 17 0.25 16</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G I 29 1 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H I 19 >=4 16</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I S 18 0.25 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J S 18 2 2</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] -0.08488745 -0.47455213 -0.28834263 0.92954003 0.44478586 0.07490685</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.82469031 -0.04972854 -0.23217610 -1.14423619</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.91414006 -0.17605318 0.09856581 -0.54009185 0.24439443 -0.45907292</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.50845312 0.40655103 -0.70032567 -0.29656083</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 +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 23 8 1 -0.28834263 0.00000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 I R 20 0.25 4 -0.23217610 0.05616652</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 B S 20 0.25 16 -0.47455213 0.18620951</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 A S 26 1 8 -0.08488745 0.20345517</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 H R 26 0.25 2 -0.04972854 0.23861409</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F R 23 8 0.5 0.07490685 0.36324947</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 E R 31 0.25 8 0.44478586 0.73312849</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 J I 17 1 <=0.25 -1.14423619 0.85589357</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 G R 31 16 2 0.82469031 1.11303293</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 D R 30 4 16 0.92954003 1.21788265</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 20 1 16 0.09856581 0.0000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 E R 25 1 0.5 0.24439443 0.1458286</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 B S 21 0.5 8 -0.17605318 0.2746190</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 H I 19 >=4 16 0.40655103 0.3079852</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 J S 18 2 2 -0.29656083 0.3951266</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 G I 29 1 8 0.50845312 0.4098873</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 F I 17 0.25 16 -0.45907292 0.5576387</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 D S 23 0.25 2 -0.54009185 0.6386577</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I S 18 0.25 4 -0.70032567 0.7988915</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 A R 26 1 8 0.91414006 0.8155742</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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