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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-0.4.2/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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||||
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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="">1.8.1.9049</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9004</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">
|
||||
@ -195,10 +195,10 @@
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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 0.001 0.25 >=128 0.025 1 0.5 0.005 1 16 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.25 256 16 0.001 8 8 0.002 8 0.0625 16 </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] -0.41123292 -1.57568929 -0.02085462 1.73584774 -0.66925895 0.36952368</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 0.17433453 -1.12247412 0.36952368 1.15028028</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -0.3351460 1.3348700 0.6668636 -1.6654448 0.4998620 0.4998620</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] -1.4984432 0.4998620 -0.6691492 0.6668636</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>
|
||||
@ -208,38 +208,38 @@
|
||||
<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 2 2 <=0.25 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 B 4 2 2 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 C >=16 2 <=0.25 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 D <=1 0.25 2 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 E >=16 <=0.125 <=0.25 0.25</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 F >=16 <=0.125 4 >=16</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 G <=1 2 <=0.25 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 H 4 0.25 4 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 I <=1 1 0.5 >=16</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 J 8 2 0.5 >=16</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 2 1 8</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 B 8 2 1 8</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 C 4 0.25 >=4 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 D <=1 0.125 0.5 0.5</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 E <=1 0.5 2 8</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 F <=1 0.25 >=4 <=0.25</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 G 4 >=4 2 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 H 4 0.25 >=4 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 I 8 1 2 0.5</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 J 4 0.5 2 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> "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] -0.15641280 0.42857996 0.14992674 -0.42197963 -0.81679006 0.57661476</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] -0.30349990 0.01816313 -0.02817569 0.55357349</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.40198724 0.61497293 0.04169761 -1.42617241 -0.07813388 -0.65411731</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 0.53631944 0.17661937 0.17391127 0.21291573</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> 5 E >=16 <=0.125 <=0.25 0.25 -0.81679006</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 D <=1 0.25 2 2 -0.42197963</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 G <=1 2 <=0.25 4 -0.30349990</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 A 2 2 <=0.25 4 -0.15641280</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 I <=1 1 0.5 >=16 -0.02817569</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 H 4 0.25 4 2 0.01816313</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 C >=16 2 <=0.25 2 0.14992674</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 B 4 2 2 4 0.42857996</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 J 8 2 0.5 >=16 0.55357349</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 F >=16 <=0.125 4 >=16 0.57661476</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> 4 D <=1 0.125 0.5 0.5 -1.42617241</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 F <=1 0.25 >=4 <=0.25 -0.65411731</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 E <=1 0.5 2 8 -0.07813388</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 C 4 0.25 >=4 1 0.04169761</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 I 8 1 2 0.5 0.17391127</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 H 4 0.25 >=4 2 0.17661937</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 J 4 0.5 2 4 0.21291573</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 A 4 2 1 8 0.40198724</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 G 4 >=4 2 2 0.53631944</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 B 8 2 1 8 0.61497293</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>
|
||||
@ -251,17 +251,17 @@
|
||||
<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 2 <=0.25 2 0.14992674 0.0000000</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 H 4 0.25 4 2 0.01816313 0.1317636</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 I <=1 1 0.5 >=16 -0.02817569 0.1781024</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 B 4 2 2 4 0.42857996 0.2786532</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 A 2 2 <=0.25 4 -0.15641280 0.3063395</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 J 8 2 0.5 >=16 0.55357349 0.4036468</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 F >=16 <=0.125 4 >=16 0.57661476 0.4266880</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 G <=1 2 <=0.25 4 -0.30349990 0.4534266</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 D <=1 0.25 2 2 -0.42197963 0.5719064</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 E >=16 <=0.125 <=0.25 0.25 -0.81679006 0.9667168</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 4 0.25 >=4 1 0.04169761 0.0000000</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 E <=1 0.5 2 8 -0.07813388 0.1198315</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 I 8 1 2 0.5 0.17391127 0.1322137</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 H 4 0.25 >=4 2 0.17661937 0.1349218</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 J 4 0.5 2 4 0.21291573 0.1712181</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 A 4 2 1 8 0.40198724 0.3602896</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 G 4 >=4 2 2 0.53631944 0.4946218</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 B 8 2 1 8 0.61497293 0.5732753</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 F <=1 0.25 >=4 <=0.25 -0.65411731 0.6958149</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 D <=1 0.125 0.5 0.5 -1.42617241 1.4678700</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>
|
||||
@ -301,7 +301,7 @@
|
||||
</div>
|
||||
|
||||
<div class="pkgdown-footer-right">
|
||||
<p></p><p><a target="_blank" href="https://www.rug.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/logos/logo_rug.svg" style="max-width: 200px;"></a></p>
|
||||
<p></p><p><a target="_blank" href="https://www.rug.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/logos/logo_rug.svg" style="max-width: 150px;"></a></p>
|
||||
</div>
|
||||
|
||||
</footer></div>
|
||||
|
||||
Reference in New Issue
Block a user