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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.rawgit.com/afeld/bootstrap-toc/v1.0.1/dist/bootstrap-toc.min.js"></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="">1.8.2.9052</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9053</small>
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|
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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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@ -200,10 +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] 0.0625 0.0625 1 0.025 8 32 0.5 >=128 0.002 0.0625</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.002 0.5 0.005 0.005 1 0.005 32 0.0625 1 >=64 </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] -0.55349668 -0.55349668 0.24542211 -0.81752498 0.84461119 1.24407059</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 0.04569241 1.64352998 -1.54531126 -0.55349668</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -1.1714935 0.2920876 -0.9286111 -0.9286111 0.4758210 -0.9286111</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 1.3944883 -0.2591128 0.4758210 1.5782217</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>
|
||||
@ -213,38 +213,38 @@
|
||||
<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">#></span> id amox cipr gent tobr</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 A 4 0.5 2 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 B 1 1 2 <=0.5</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 C >=16 0.5 2 >=16</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 D 4 0.25 >=4 <=0.5</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 E 2 <=0.125 2 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 F 2 <=0.125 2 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 G >=16 <=0.125 >=4 >=16</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 H 8 1 >=4 >=16</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 I 1 0.5 1 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 J >=16 0.5 >=4 4</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 16 0.0625 4 <=0.5</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 B 4 4 8 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 C 32 2 0.5 <=0.5</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 D 32 2 2 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 E 16 4 8 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 F 16 1 8 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 G 4 0.125 1 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 H <=2 0.5 >=16 <=0.5</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 I 32 1 4 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 J 16 1 4 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">#></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] -0.02072625 -0.53283992 0.56658881 -0.27325161 -0.60171721 -0.60171721</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 0.51272334 0.99239255 -0.70457864 0.66312613</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -0.69810970 0.10645099 -0.38692709 0.41316947 0.69213408 0.44073351</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] -0.54222633 -0.51743382 0.45152367 0.04068523</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> 9 I 1 0.5 1 4 -0.70457864</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 E 2 <=0.125 2 4 -0.60171721</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 F 2 <=0.125 2 4 -0.60171721</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 B 1 1 2 <=0.5 -0.53283992</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 D 4 0.25 >=4 <=0.5 -0.27325161</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 A 4 0.5 2 4 -0.02072625</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 G >=16 <=0.125 >=4 >=16 0.51272334</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 C >=16 0.5 2 >=16 0.56658881</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 J >=16 0.5 >=4 4 0.66312613</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 H 8 1 >=4 >=16 0.99239255</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> 1 A 16 0.0625 4 <=0.5 -0.69810970</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 G 4 0.125 1 4 -0.54222633</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 H <=2 0.5 >=16 <=0.5 -0.51743382</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 C 32 2 0.5 <=0.5 -0.38692709</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 J 16 1 4 1 0.04068523</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 B 4 4 8 1 0.10645099</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 D 32 2 2 2 0.41316947</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 F 16 1 8 2 0.44073351</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 I 32 1 4 2 0.45152367</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 E 16 4 8 2 0.69213408</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>
|
||||
@ -256,17 +256,17 @@
|
||||
<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" 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 0.5 2 >=16 0.56658881 0.00000000</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 G >=16 <=0.125 >=4 >=16 0.51272334 0.05386547</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 J >=16 0.5 >=4 4 0.66312613 0.09653732</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 H 8 1 >=4 >=16 0.99239255 0.42580374</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 A 4 0.5 2 4 -0.02072625 0.58731506</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 D 4 0.25 >=4 <=0.5 -0.27325161 0.83984042</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 B 1 1 2 <=0.5 -0.53283992 1.09942873</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 E 2 <=0.125 2 4 -0.60171721 1.16830602</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 F 2 <=0.125 2 4 -0.60171721 1.16830602</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 I 1 0.5 1 4 -0.70457864 1.27116745</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 32 2 0.5 <=0.5 -0.38692709 0.0000000</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 H <=2 0.5 >=16 <=0.5 -0.51743382 0.1305067</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 G 4 0.125 1 4 -0.54222633 0.1552992</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 A 16 0.0625 4 <=0.5 -0.69810970 0.3111826</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 J 16 1 4 1 0.04068523 0.4276123</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 B 4 4 8 1 0.10645099 0.4933781</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 D 32 2 2 2 0.41316947 0.8000966</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 F 16 1 8 2 0.44073351 0.8276606</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 I 32 1 4 2 0.45152367 0.8384508</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 E 16 4 8 2 0.69213408 1.0790612</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>
|
||||
@ -276,9 +276,9 @@
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>d <span class="op">=</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">.</span>, <span class="fu">where</span><span class="op">(</span><span class="va">is.rsi</span><span class="op">)</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/arrange.html" class="external-link">arrange</a></span><span class="op">(</span><span class="va">mo</span>, <span class="va">d</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Using column 'mo' as input for `mo_genus()`</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Using column 'mo' as input for `mo_species()`</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Using column 'mo' as input for mo_genus()</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Using column 'mo' as input for mo_species()</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem)</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Calculating mean AMR distance based on columns "IPM", "MEM" and "TCY"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 63 × 5</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Groups: mo [4]</span></span>
|
||||
|
||||
Reference in New Issue
Block a user