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Built site for AMR: 1.8.2.9074@1db74e8

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2022-12-29 15:31:17 +00:00
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reference/mean_amr_distance.html
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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="">1.8.2.9073</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9074</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">
@ -200,10 +200,11 @@
<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] 0.5 0.0625 0.0625 64 64 2 &gt;=256 &gt;=256 0.125 0.0625</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.125 1 0.125 16 0.5 0.005 0.025 0.25 &gt;=32 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] &lt;=0.001</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] -0.44345719 -1.02187960 -1.02187960 0.90619512 0.90619512 -0.05784224</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 1.29181006 1.29181006 -0.82907213 -1.02187960</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.15089674 0.48954269 -0.15089674 1.34346192 0.27606288 -1.14226627</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.64658150 0.06258307 1.55694173 -1.63795104</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>
@ -213,38 +214,38 @@
<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 &gt;=64 1 &gt;=4 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B 16 0.5 2 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C 4 &lt;=0.25 1 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D 32 &gt;=2 &lt;=0.5 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 16 &lt;=0.25 &gt;=4 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F 16 &lt;=0.25 &gt;=4 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G 32 &gt;=2 &gt;=4 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 &lt;=2 1 &gt;=4 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J &gt;=64 &gt;=2 2 2</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 2 &lt;=1 &lt;=1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B &lt;=2 2 16 &lt;=1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C &gt;=16 &gt;=4 2 &lt;=1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D &gt;=16 0.125 2 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 4 &gt;=4 &lt;=1 8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F 4 &gt;=4 8 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G &lt;=2 0.125 2 &lt;=1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H &gt;=16 0.25 &lt;=1 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I &gt;=16 0.25 8 8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J &lt;=2 0.5 &lt;=1 &lt;=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] 0.81284429 -0.28991150 -1.03511883 -0.22702202 0.11273878 0.11273878</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.85671083 -0.80055308 0.04737875 0.41019401</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.18987114 0.10887987 0.28105302 -0.11068834 0.34470481 0.44567516</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.86673217 0.04090765 0.74321579 -0.79714465</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> 3 C 4 &lt;=0.25 1 2 -1.03511883</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H 8 0.5 2 1 -0.80055308</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B 16 0.5 2 2 -0.28991150</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D 32 &gt;=2 &lt;=0.5 2 -0.22702202</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I &lt;=2 1 &gt;=4 4 0.04737875</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 16 &lt;=0.25 &gt;=4 4 0.11273878</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F 16 &lt;=0.25 &gt;=4 4 0.11273878</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J &gt;=64 &gt;=2 2 2 0.41019401</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A &gt;=64 1 &gt;=4 4 0.81284429</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G 32 &gt;=2 &gt;=4 4 0.85671083</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> 7 G &lt;=2 0.125 2 &lt;=1 -0.86673217</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J &lt;=2 0.5 &lt;=1 &lt;=1 -0.79714465</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A 8 2 &lt;=1 &lt;=1 -0.18987114</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D &gt;=16 0.125 2 2 -0.11068834</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H &gt;=16 0.25 &lt;=1 4 0.04090765</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B &lt;=2 2 16 &lt;=1 0.10887987</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C &gt;=16 &gt;=4 2 &lt;=1 0.28105302</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 4 &gt;=4 &lt;=1 8 0.34470481</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F 4 &gt;=4 8 2 0.44567516</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I &gt;=16 0.25 8 8 0.74321579</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>
@ -256,17 +257,17 @@
<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 4 &lt;=0.25 1 2 -1.03511883 0.0000000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 H 8 0.5 2 1 -0.80055308 0.2345657</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 B 16 0.5 2 2 -0.28991150 0.7452073</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D 32 &gt;=2 &lt;=0.5 2 -0.22702202 0.8080968</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 I &lt;=2 1 &gt;=4 4 0.04737875 1.0824976</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 E 16 &lt;=0.25 &gt;=4 4 0.11273878 1.1478576</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 F 16 &lt;=0.25 &gt;=4 4 0.11273878 1.1478576</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 J &gt;=64 &gt;=2 2 2 0.41019401 1.4453128</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 A &gt;=64 1 &gt;=4 4 0.81284429 1.8479631</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 G 32 &gt;=2 &gt;=4 4 0.85671083 1.8918297</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 &gt;=16 &gt;=4 2 &lt;=1 0.28105302 0.00000000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 E 4 &gt;=4 &lt;=1 8 0.34470481 0.06365179</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 F 4 &gt;=4 8 2 0.44567516 0.16462214</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 B &lt;=2 2 16 &lt;=1 0.10887987 0.17217315</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 H &gt;=16 0.25 &lt;=1 4 0.04090765 0.24014537</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 D &gt;=16 0.125 2 2 -0.11068834 0.39174136</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 I &gt;=16 0.25 8 8 0.74321579 0.46216277</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 A 8 2 &lt;=1 &lt;=1 -0.18987114 0.47092416</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 J &lt;=2 0.5 &lt;=1 &lt;=1 -0.79714465 1.07819767</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 G &lt;=2 0.125 2 &lt;=1 -0.86673217 1.14778519</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>