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Built site for AMR: 1.8.2.9044@2d90218

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2022-11-05 11:15:23 +00:00
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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="">1.8.2.9043</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9044</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">
@ -195,10 +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] 64 16 &gt;=128 0.025 32 64 0.125 0.005 8 0.005</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.01 32 2 &gt;=128 8 32 16 8 0.5 0.25 </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] 0.8826792 0.5471212 1.0504581 -1.0169023 0.7149002 0.8826792</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.6273316 -1.4064731 0.3793422 -1.4064731</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -2.0808837 0.7765483 -0.2050619 1.2673534 0.2857432 0.7765483</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.5311458 0.2857432 -0.6958670 -0.9412696</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>
@ -208,38 +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 16 &lt;=0.25 &gt;=8 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B 32 &gt;=2 &gt;=8 &lt;=0.5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C 32 1 &gt;=8 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D &lt;=1 1 1 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 4 &gt;=2 &gt;=8 &gt;=4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F 4 &lt;=0.25 &gt;=8 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G 8 &lt;=0.25 &lt;=0.5 &gt;=4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H &lt;=1 &gt;=2 1 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I &lt;=1 &lt;=0.25 4 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J 32 &lt;=0.25 &gt;=8 1</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 &gt;=4 4 &gt;=4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B 32 0.125 1 0.5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C 4 0.5 4 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D 32 0.25 4 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 4 0.25 0.25 0.25</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F 32 0.0625 0.25 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G 32 1 0.5 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H 32 0.25 0.5 0.5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I 16 1 1 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J 4 0.125 0.25 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] 0.00491141 0.39299678 0.47548368 -0.32590689 0.81532985 -0.23108238</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.22244389 -0.40839379 -0.62380306 0.12290831</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1.0408682 -0.2106031 0.2372580 0.6330929 -1.1062738 -0.2408099</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.2660010 -0.2183470 0.4388309 -0.8400171</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> 9 I &lt;=1 &lt;=0.25 4 1 -0.62380306</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H &lt;=1 &gt;=2 1 1 -0.40839379</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D &lt;=1 1 1 2 -0.32590689</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F 4 &lt;=0.25 &gt;=8 1 -0.23108238</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G 8 &lt;=0.25 &lt;=0.5 &gt;=4 -0.22244389</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A 16 &lt;=0.25 &gt;=8 1 0.00491141</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J 32 &lt;=0.25 &gt;=8 1 0.12290831</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B 32 &gt;=2 &gt;=8 &lt;=0.5 0.39299678</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C 32 1 &gt;=8 1 0.47548368</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 4 &gt;=2 &gt;=8 &gt;=4 0.81532985</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> 5 E 4 0.25 0.25 0.25 -1.1062738</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J 4 0.125 0.25 1 -0.8400171</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F 32 0.0625 0.25 2 -0.2408099</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H 32 0.25 0.5 0.5 -0.2183470</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B 32 0.125 1 0.5 -0.2106031</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C 4 0.5 4 2 0.2372580</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G 32 1 0.5 1 0.2660010</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I 16 1 1 2 0.4388309</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D 32 0.25 4 2 0.6330929</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A 8 &gt;=4 4 &gt;=4 1.0408682</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>
@ -251,17 +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 32 1 &gt;=8 1 0.47548368 0.0000000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B 32 &gt;=2 &gt;=8 &lt;=0.5 0.39299678 0.0824869</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 E 4 &gt;=2 &gt;=8 &gt;=4 0.81532985 0.3398462</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 J 32 &lt;=0.25 &gt;=8 1 0.12290831 0.3525754</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 A 16 &lt;=0.25 &gt;=8 1 0.00491141 0.4705723</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 G 8 &lt;=0.25 &lt;=0.5 &gt;=4 -0.22244389 0.6979276</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 F 4 &lt;=0.25 &gt;=8 1 -0.23108238 0.7065661</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 D &lt;=1 1 1 2 -0.32590689 0.8013906</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 H &lt;=1 &gt;=2 1 1 -0.40839379 0.8838775</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 I &lt;=1 &lt;=0.25 4 1 -0.62380306 1.0992867</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 4 0.5 4 2 0.2372580 0.00000000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 G 32 1 0.5 1 0.2660010 0.02874298</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 I 16 1 1 2 0.4388309 0.20157281</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D 32 0.25 4 2 0.6330929 0.39583483</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 B 32 0.125 1 0.5 -0.2106031 0.44786118</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 H 32 0.25 0.5 0.5 -0.2183470 0.45560507</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 F 32 0.0625 0.25 2 -0.2408099 0.47806797</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 A 8 &gt;=4 4 &gt;=4 1.0408682 0.80361015</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 J 4 0.125 0.25 1 -0.8400171 1.07727511</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 E 4 0.25 0.25 0.25 -1.1062738 1.34353185</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>