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<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Calculates a normalised mean for antimicrobial resistance between multiple observations, to help to identify similar isolates without comparing antibiograms by hand."><title>Calculate the Mean AMR Distance — mean_amr_distance • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Fira_Code-0.4.8/font.css" rel="stylesheet"><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Calculate the Mean AMR Distance — mean_amr_distance"><meta property="og:description" content="Calculates a normalised mean for antimicrobial resistance between multiple observations, to help to identify similar isolates without comparing antibiograms by hand."><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"><meta name="twitter:card" content="summary_large_image"><meta name="twitter:creator" content="@msberends"><meta name="twitter:site" content="@msberends"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
|
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<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
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<![endif]--></head><body>
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@ -218,30 +218,30 @@
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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>
|
||||
<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] S R R R R S S I I R</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] R S I I S I I R I I</span>
|
||||
<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>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -0.9486833 0.9486833 0.9486833 0.9486833 0.9486833 -0.9486833</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] -0.9486833 -0.9486833 -0.9486833 0.9486833</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 1.8973666 -0.4743416 -0.4743416 -0.4743416 -0.4743416 -0.4743416</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] -0.4743416 1.8973666 -0.4743416 -0.4743416</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<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>
|
||||
<span class="r-in"><span><span class="va">mic</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'mic'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 64 0.01 0.125 0.25 >=256 0.0625 0.25 32 4 0.5 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.002 0.5 0.125 128 0.25 0.5 256 0.125 0.125 64 </span>
|
||||
<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>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 1.2031622 -1.4359065 -0.6753484 -0.4666250 1.6206090 -0.8840718</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] -0.4666250 0.9944388 0.3682686 -0.2579016</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -1.6429088 -0.1673475 -0.5378223 1.3145519 -0.3525849 -0.1673475</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 1.4997893 -0.5378223 -0.5378223 1.1293145</span>
|
||||
<span class="r-in"><span><span class="co"># equal to the Z-score of their log2:</span></span></span>
|
||||
<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>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 1.2031622 -1.4359065 -0.6753484 -0.4666250 1.6206090 -0.8840718</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] -0.4666250 0.9944388 0.3682686 -0.2579016</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -1.6429088 -0.1673475 -0.5378223 1.3145519 -0.3525849 -0.1673475</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 1.4997893 -0.5378223 -0.5378223 1.1293145</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<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>
|
||||
<span class="r-in"><span><span class="va">disk</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'disk'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 15 42 36 45 47 50 16 25 43 49</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 40 45 43 14 42 40 37 15 42 11</span>
|
||||
<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>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -1.63113065 0.38907704 -0.05985801 0.61354456 0.76318957 0.98765709</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] -1.55630815 -0.88290558 0.46389954 0.91283459</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.5182957 0.8832927 0.7372939 -1.3796886 0.6642945 0.5182957</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 0.2992975 -1.3066892 0.6642945 -1.5986868</span>
|
||||
<span class="r-in"><span></span></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/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>
|
||||
@ -251,22 +251,22 @@
|
||||
<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">#></span> id amox cipr gent tobr</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 A I 26 >=8 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 B S 26 2 0.5</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 C R 26 2 >=4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 D I 28 <=1 0.25</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 E I 21 <=1 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 F S 29 4 >=4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 G I 22 2 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 H I 29 4 >=4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 I I 26 4 0.25</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 J R 17 >=8 0.25</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 A R 17 <=0.5 >=8</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 B I 26 <=0.5 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 C R 18 4 >=8</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 D R 22 <=0.5 <=0.5</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 E I 30 <=0.5 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 F S 18 4 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 G I 26 8 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 H S 29 8 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 I I 22 16 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 J S 31 1 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">#></span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> and "tobr"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.423532301 -0.328588957 0.698154916 -0.575069322 -0.739389038</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [6] 0.531053275 -0.298538277 0.531053275 -0.241739536 -0.000468637</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.12957466 -0.14083442 0.55230568 -0.36152662 -0.31478853 -0.33012168</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 0.17672648 0.13748045 -0.07163669 0.22282068</span>
|
||||
<span class="r-in"><span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span> <span class="op"><-</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span>, <span class="fu"><a href="https://tidyselect.r-lib.org/reference/where.html" class="external-link">where</a></span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in .subset(x, j):</span> invalid subscript type 'list'</span>
|
||||
<span class="r-in"><span><span class="va">y</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/order.html" class="external-link">order</a></span><span class="op">(</span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span><span class="op">)</span>, <span class="op">]</span></span></span>
|
||||
@ -282,17 +282,17 @@
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> and "tobr"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr amr_distance check_id_C</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 C R 26 2 >=4 0.698154916 0.0000000</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 F S 29 4 >=4 0.531053275 0.1671016</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 H I 29 4 >=4 0.531053275 0.1671016</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 A I 26 >=8 2 0.423532301 0.2746226</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 J R 17 >=8 0.25 -0.000468637 0.6986236</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 I I 26 4 0.25 -0.241739536 0.9398945</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 G I 22 2 2 -0.298538277 0.9966932</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 B S 26 2 0.5 -0.328588957 1.0267439</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 D I 28 <=1 0.25 -0.575069322 1.2732242</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 E I 21 <=1 1 -0.739389038 1.4375440</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr amr_distance check_id_C</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 C R 18 4 >=8 0.55230568 0.0000000</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 J S 31 1 4 0.22282068 0.3294850</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 G I 26 8 2 0.17672648 0.3755792</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 H S 29 8 1 0.13748045 0.4148252</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 A R 17 <=0.5 >=8 0.12957466 0.4227310</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 I I 22 16 1 -0.07163669 0.6239424</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 B I 26 <=0.5 4 -0.14083442 0.6931401</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 E I 30 <=0.5 1 -0.31478853 0.8670942</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 F S 18 4 2 -0.33012168 0.8824274</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 D R 22 <=0.5 <=0.5 -0.36152662 0.9138323</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">%>%</a></span></span></span>
|
||||
|
||||
Reference in New Issue
Block a user