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Built site for AMR: 1.8.2.9138@dad2530
This commit is contained in:
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@@ -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="">1.8.2.9137</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9138</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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@@ -170,7 +170,7 @@
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<dt>combine_SI</dt>
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<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether all values of S and I must be merged into one, so the input only consists of S+I vs. R (susceptible vs. resistant), defaults to <code>TRUE</code></p></dd>
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<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether all values of S and I must be merged into one, so the input only consists of S+I vs. R (susceptible vs. resistant) - the default is <code>TRUE</code></p></dd>
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<dt>amr_distance</dt>
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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] R I S S S S S S R S</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] R R S R R I R S 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">sir</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 1.8973666 -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] -0.4743416 -0.4743416 1.8973666 -0.4743416</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 0.001 0.01 1 4 0.125 0.125 8 2 0.0625</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.0625 0.0625 0.5 >=64 >=64 0.01 0.025 0.5 4 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] 0.06516456 -1.92394777 -1.09443897 0.56457861 1.06399267 -0.18454247</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.18454247 1.31369970 0.81428564 -0.43424950</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.65023906 -0.65023906 0.02162933 1.58932224 1.58932224 -1.24234686</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.94629296 0.02162933 0.69349772 -0.42628293</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] 0.06516456 -1.92394777 -1.09443897 0.56457861 1.06399267 -0.18454247</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.18454247 1.31369970 0.81428564 -0.43424950</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.65023906 -0.65023906 0.02162933 1.58932224 1.58932224 -1.24234686</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.94629296 0.02162933 0.69349772 -0.42628293</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] 12 30 18 33 24 27 16 46 50 32</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 18 50 28 16 21 46 35 38 41 42</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] -1.36485665 0.09748976 -0.87740785 0.34121416 -0.38995904 -0.14623464</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -1.03989078 1.39735324 1.72231911 0.25997270</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -1.2835219 1.3663298 -0.4554433 -1.4491377 -1.0350983 1.0350983</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.1242118 0.3726354 0.6210590 0.7038669</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 R 24 4 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B S 20 <=0.5 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C S 26 1 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D S 21 <=0.5 >=16</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E R 26 2 <=0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F S 18 4 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G R 21 2 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H S 29 2 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I R 23 1 <=0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J R 19 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 S 31 8 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B R 31 0.5 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C R 19 <=0.25 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D I 23 1 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E R 18 8 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F I 28 1 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G S 29 0.5 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H I 17 >=16 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I I 26 <=0.25 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J I 30 <=0.25 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] 0.584051604 -0.989329211 0.140243831 -0.328508012 0.257166131</span>
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<span class="r-out co"><span class="r-pr">#></span> [6] -0.197313482 0.138976310 0.585319125 -0.187909163 -0.002697134</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",</span>
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<span class="r-msg co"><span class="r-pr">#></span> and "tobr"</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.2343675231 0.3170884159 0.3733587992 -0.4531732369 0.1646099199</span>
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<span class="r-out co"><span class="r-pr">#></span> [6] -0.2272860166 -0.2908156418 0.0641437661 -0.1815016525 -0.0007918763</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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@@ -263,19 +263,19 @@
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<span class="r-in"><span> <span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
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<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/arrange.html" class="external-link">arrange</a></span><span class="op">(</span><span class="va">check_id_C</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-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 26 1 8 0.140243831 0.000000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 G R 21 2 1 0.138976310 0.001267521</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 E R 26 2 <=0.25 0.257166131 0.116922299</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 J R 19 2 1 -0.002697134 0.142940965</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 I R 23 1 <=0.25 -0.187909163 0.328152995</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F S 18 4 2 -0.197313482 0.337557314</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 A R 24 4 1 0.584051604 0.443807773</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H S 29 2 8 0.585319125 0.445075294</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 D S 21 <=0.5 >=16 -0.328508012 0.468751843</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 B S 20 <=0.5 0.5 -0.989329211 1.129573042</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",</span>
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<span class="r-msg co"><span class="r-pr">#></span> and "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 19 <=0.25 4 0.3733587992 0.00000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B R 31 0.5 1 0.3170884159 0.05627038</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 A S 31 8 1 0.2343675231 0.13899128</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 E R 18 8 1 0.1646099199 0.20874888</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 H I 17 >=16 2 0.0641437661 0.30921503</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 J I 30 <=0.25 2 -0.0007918763 0.37415068</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 I I 26 <=0.25 2 -0.1815016525 0.55486045</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 F I 28 1 1 -0.2272860166 0.60064482</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 G S 29 0.5 1 -0.2908156418 0.66417444</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 D I 23 1 1 -0.4531732369 0.82653204</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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@@ -288,7 +288,7 @@
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<span class="r-msg co"><span class="r-pr">#></span> ℹ Using column 'mo' as input for mo_genus()</span>
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<span class="r-msg co"><span class="r-pr">#></span> ℹ Using column 'mo' as input for mo_species()</span>
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<span class="r-msg co"><span class="r-pr">#></span> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem)</span>
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<span class="r-msg co"><span class="r-pr">#></span> ℹ Calculating mean AMR distance based on columns "TCY", "IPM" and "MEM"</span>
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<span class="r-msg co"><span class="r-pr">#></span> ℹ Calculating mean AMR distance based on columns "TCY", "IPM", and "MEM"</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 63 × 5</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Groups: mo [4]</span></span>
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<span class="r-out co"><span class="r-pr">#></span> mo TCY IPM MEM dist</span>
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