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Built site for AMR: 1.8.2.9041@d20caae

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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9040</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9041</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -195,11 +195,10 @@
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">x</span> <span class="op">&lt;-</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>
<span class="r-in"><span><span class="va">x</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 32 128 &lt;=0.001 0.125 0.025 16 0.01 16 64 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 0.01 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 16 0.25 0.005 1 0.125 0.01 0.0625 16 8 4 </span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.8741078 1.1886741 -1.4797580 -0.3841574 -0.7493576 0.7168247</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.9572746 0.7168247 1.0313910 -0.9572746</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1.1709756 -0.2261557 -1.5403570 0.2395547 -0.4590109 -1.3075018</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.6918661 1.1709756 0.9381204 0.7052652</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">y</span> <span class="op">&lt;-</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>
<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>
@ -209,38 +208,38 @@
<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>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">y</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A 2 0.5 2 &gt;=4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B 16 1 &gt;=4 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C 8 &gt;=2 2 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D 1 0.25 2 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 1 1 &gt;=4 &gt;=4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F 1 0.25 2 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G 2 1 &gt;=4 &gt;=4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H 8 0.5 2 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I 4 &gt;=2 &gt;=4 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J 16 0.25 2 &gt;=4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A 8 0.125 2 &lt;=0.5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B &gt;=16 &gt;=2 &gt;=4 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C 8 0.5 &lt;=0.5 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D &gt;=16 0.0625 &gt;=4 &lt;=0.5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 8 0.0625 1 8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F 8 0.0625 1 8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G 8 0.5 &gt;=4 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H 4 0.0625 &lt;=0.5 &lt;=0.5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I &gt;=16 0.25 &lt;=0.5 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J &gt;=16 1 1 1</span>
<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>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> "id" and "tobr"</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>NAs introduced by coercion</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.1488052 0.6945257 0.2690034 -1.1500416 0.3939183 -0.8331088</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.5483034 -0.4739008 0.5987413 0.1013643</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.37716248 1.03332464 -0.35122411 0.05745946 -0.09068362 -0.09068362</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.55047307 -1.27626480 0.19452559 0.35023586</span>
<span class="r-in"><span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span> <span class="op">&lt;-</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span>, <span class="fu">where</span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent" and</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> "tobr"</span>
<span class="r-in"><span><span class="va">y</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/order.html" class="external-link">order</a></span><span class="op">(</span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span><span class="op">)</span>, <span class="op">]</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr amr_distance</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D 1 0.25 2 1 -1.1500416</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F 1 0.25 2 2 -0.8331088</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H 8 0.5 2 1 -0.4739008</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A 2 0.5 2 &gt;=4 -0.1488052</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J 16 0.25 2 &gt;=4 0.1013643</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C 8 &gt;=2 2 2 0.2690034</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 1 1 &gt;=4 &gt;=4 0.3939183</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G 2 1 &gt;=4 &gt;=4 0.5483034</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I 4 &gt;=2 &gt;=4 2 0.5987413</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B 16 1 &gt;=4 2 0.6945257</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr amr_distance</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H 4 0.0625 &lt;=0.5 &lt;=0.5 -1.27626480</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A 8 0.125 2 &lt;=0.5 -0.37716248</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C 8 0.5 &lt;=0.5 1 -0.35122411</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 8 0.0625 1 8 -0.09068362</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F 8 0.0625 1 8 -0.09068362</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D &gt;=16 0.0625 &gt;=4 &lt;=0.5 0.05745946</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I &gt;=16 0.25 &lt;=0.5 4 0.19452559</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J &gt;=16 1 1 1 0.35023586</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G 8 0.5 &gt;=4 4 0.55047307</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B &gt;=16 &gt;=2 &gt;=4 2 1.03332464</span>
<span class="r-in"><span></span></span>
<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>
<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">%&gt;%</a></span></span></span>
@ -252,17 +251,17 @@
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent" and</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> "tobr"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr amr_distance check_id_C</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 C 8 &gt;=2 2 2 0.2690034 0.0000000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 E 1 1 &gt;=4 &gt;=4 0.3939183 0.1249149</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 J 16 0.25 2 &gt;=4 0.1013643 0.1676392</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 G 2 1 &gt;=4 &gt;=4 0.5483034 0.2793000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 I 4 &gt;=2 &gt;=4 2 0.5987413 0.3297379</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 A 2 0.5 2 &gt;=4 -0.1488052 0.4178086</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 B 16 1 &gt;=4 2 0.6945257 0.4255223</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H 8 0.5 2 1 -0.4739008 0.7429042</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 F 1 0.25 2 2 -0.8331088 1.1021122</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 D 1 0.25 2 1 -1.1500416 1.4190451</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr amr_distance check_id_C</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 C 8 0.5 &lt;=0.5 1 -0.35122411 0.00000000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 A 8 0.125 2 &lt;=0.5 -0.37716248 0.02593837</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 E 8 0.0625 1 8 -0.09068362 0.26054049</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 F 8 0.0625 1 8 -0.09068362 0.26054049</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 D &gt;=16 0.0625 &gt;=4 &lt;=0.5 0.05745946 0.40868357</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 I &gt;=16 0.25 &lt;=0.5 4 0.19452559 0.54574970</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 J &gt;=16 1 1 1 0.35023586 0.70145997</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 G 8 0.5 &gt;=4 4 0.55047307 0.90169717</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 H 4 0.0625 &lt;=0.5 &lt;=0.5 -1.27626480 0.92504069</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 B &gt;=16 &gt;=2 &gt;=4 2 1.03332464 1.38454874</span>
<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>
<span class="r-in"><span> <span class="co"># support for groups</span></span></span>
<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">%&gt;%</a></span></span></span>