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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="This function calculates a normalised mean for antimicrobial resistance between multiple observations."><title>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-5.1.3/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.1.3/bootstrap.bundle.min.js"></script><link href="../deps/Fira_Code-0.4.4/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="Mean AMR Distance — mean_amr_distance"><meta property="og:description" content="This function calculates a normalised mean for antimicrobial resistance between multiple observations."><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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@ -10,7 +10,7 @@
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9062</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9063</small>
|
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
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@ -200,11 +200,10 @@
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||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">x</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">x</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] 0.125 4 0.025 32 <=0.001 128 0.002 16 <=0.001</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [10] 1 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 1 0.0625 0.001 0.001 0.5 0.5 0.125 32 0.125 32 </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">#></span> [1] -0.1673708 0.6088797 -0.5278503 1.0746300 -1.2488094 1.3851301</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] -1.0935593 0.9193799 -1.2488094 0.2983795</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.4278030 -0.3524476 -1.5161494 -1.5161494 0.2327404 0.2327404</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] -0.1573850 1.4031163 -0.1573850 1.4031163</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>
|
||||
@ -215,37 +214,37 @@
|
||||
<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 >=64 4 1 0.5</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 B 4 1 >=4 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 C 16 <=0.125 >=4 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 D 8 2 2 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 E 32 1 1 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 F 8 0.25 >=4 0.5</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 G >=64 0.5 2 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 H 4 0.5 >=4 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 I >=64 2 1 0.5</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 J 16 <=0.125 2 0.5</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 A 8 4 >=16 8</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 B 8 0.25 0.5 0.25</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 C 16 0.25 0.25 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 D 16 4 0.5 0.25</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 E >=32 1 0.5 8</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 F 8 <=0.125 >=16 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 G 16 0.25 1 0.25</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 H 4 0.5 4 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 I 16 4 0.25 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 J 8 0.25 1 8</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> "id" and "tobr"</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>NAs introduced by coercion</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.12023536 0.33318132 0.20872945 0.16343985 -0.14151184 -0.36277928</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 0.52860021 -0.18662082 -0.02573319 -0.63754106</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.877285110 -0.776502449 -0.356795921 0.029167509 0.657578311</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [6] 0.001921626 -0.371866780 -0.139430735 0.154699834 -0.076056506</span>
|
||||
<span class="r-in"><span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span> <span class="op"><-</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span>, <span class="fu">where</span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent" and</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> "tobr"</span>
|
||||
<span class="r-in"><span><span class="va">y</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/order.html" class="external-link">order</a></span><span class="op">(</span><span class="va">y</span><span class="op">$</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">#></span> id amox cipr gent tobr amr_distance</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 J 16 <=0.125 2 0.5 -0.63754106</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 F 8 0.25 >=4 0.5 -0.36277928</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 H 4 0.5 >=4 1 -0.18662082</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 E 32 1 1 1 -0.14151184</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 I >=64 2 1 0.5 -0.02573319</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 A >=64 4 1 0.5 0.12023536</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 D 8 2 2 2 0.16343985</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 C 16 <=0.125 >=4 4 0.20872945</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 B 4 1 >=4 4 0.33318132</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 G >=64 0.5 2 4 0.52860021</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 B 8 0.25 0.5 0.25 -0.776502449</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 G 16 0.25 1 0.25 -0.371866780</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 C 16 0.25 0.25 1 -0.356795921</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 H 4 0.5 4 4 -0.139430735</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 J 8 0.25 1 8 -0.076056506</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 F 8 <=0.125 >=16 2 0.001921626</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 D 16 4 0.5 0.25 0.029167509</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 I 16 4 0.25 1 0.154699834</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 E >=32 1 0.5 8 0.657578311</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 A 8 4 >=16 8 0.877285110</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">%>%</a></span></span></span>
|
||||
@ -258,16 +257,16 @@
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent" and</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> "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 16 <=0.125 >=4 4 0.20872945 0.00000000</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 D 8 2 2 2 0.16343985 0.04528960</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 A >=64 4 1 0.5 0.12023536 0.08849408</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 B 4 1 >=4 4 0.33318132 0.12445187</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 I >=64 2 1 0.5 -0.02573319 0.23446263</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 G >=64 0.5 2 4 0.52860021 0.31987077</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 E 32 1 1 1 -0.14151184 0.35024128</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 H 4 0.5 >=4 1 -0.18662082 0.39535027</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 F 8 0.25 >=4 0.5 -0.36277928 0.57150872</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 J 16 <=0.125 2 0.5 -0.63754106 0.84627050</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 C 16 0.25 0.25 1 -0.356795921 0.00000000</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 G 16 0.25 1 0.25 -0.371866780 0.01507086</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 H 4 0.5 4 4 -0.139430735 0.21736519</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 J 8 0.25 1 8 -0.076056506 0.28073941</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 F 8 <=0.125 >=16 2 0.001921626 0.35871755</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 D 16 4 0.5 0.25 0.029167509 0.38596343</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 B 8 0.25 0.5 0.25 -0.776502449 0.41970653</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 I 16 4 0.25 1 0.154699834 0.51149575</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 E >=32 1 0.5 8 0.657578311 1.01437423</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 A 8 4 >=16 8 0.877285110 1.23408103</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