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Built site for AMR: 1.8.2.9042@3b65298

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2022-11-05 07:26:59 +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="">1.8.2.9041</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9042</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 +195,11 @@
<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] 16 0.25 0.005 1 0.125 0.01 0.0625 16 8 4 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 4 0.025 16 1 64 1 4 0.0625 &lt;=0.002</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 0.005 </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] 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-out co"><span class="r-pr">#&gt;</span> [1] 0.6331668 -0.8186885 1.0297441 0.2365895 1.4263214 0.2365895</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.6331668 -0.5565652 -1.5412239 -1.2791005</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 +209,38 @@
<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 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-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 4 0.25 4 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B 16 0.125 &lt;=2 &gt;=8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C 4 &gt;=1 &lt;=2 &lt;=1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D 8 0.125 &gt;=8 &lt;=1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 4 &gt;=1 &lt;=2 &gt;=8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F 8 &gt;=1 &gt;=8 &lt;=1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G 4 0.125 4 &gt;=8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H 8 0.0625 &lt;=2 &gt;=8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I 8 0.0625 &gt;=8 &gt;=8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J 8 0.0625 &gt;=8 4</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] -0.37716248 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-out co"><span class="r-pr">#&gt;</span> [1] -0.35825689 0.32811868 -0.50858606 -0.04827254 0.02773665 0.39214262</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.14751347 -0.18908497 0.34124511 0.16247088</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> 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-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 &gt;=1 &lt;=2 &lt;=1 -0.50858606</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A 4 0.25 4 2 -0.35825689</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H 8 0.0625 &lt;=2 &gt;=8 -0.18908497</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G 4 0.125 4 &gt;=8 -0.14751347</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D 8 0.125 &gt;=8 &lt;=1 -0.04827254</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 4 &gt;=1 &lt;=2 &gt;=8 0.02773665</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J 8 0.0625 &gt;=8 4 0.16247088</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B 16 0.125 &lt;=2 &gt;=8 0.32811868</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I 8 0.0625 &gt;=8 &gt;=8 0.34124511</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F 8 &gt;=1 &gt;=8 &lt;=1 0.39214262</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 +252,17 @@
<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 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-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 &gt;=1 &lt;=2 &lt;=1 -0.50858606 0.0000000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 A 4 0.25 4 2 -0.35825689 0.1503292</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 H 8 0.0625 &lt;=2 &gt;=8 -0.18908497 0.3195011</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 G 4 0.125 4 &gt;=8 -0.14751347 0.3610726</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 D 8 0.125 &gt;=8 &lt;=1 -0.04827254 0.4603135</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 E 4 &gt;=1 &lt;=2 &gt;=8 0.02773665 0.5363227</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 J 8 0.0625 &gt;=8 4 0.16247088 0.6710569</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 B 16 0.125 &lt;=2 &gt;=8 0.32811868 0.8367047</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I 8 0.0625 &gt;=8 &gt;=8 0.34124511 0.8498312</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 F 8 &gt;=1 &gt;=8 &lt;=1 0.39214262 0.9007287</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>