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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-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/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="">1.8.2.9065</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9066</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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@ -200,10 +200,11 @@
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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] 0.025 0.005 0.01 4 4 8 1 >=16 0.001 0.125</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] <=0.001 0.0625 0.01 0.005 32 0.01 4 0.025 2 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [10] 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] -0.6319520 -1.0956588 -0.8959511 0.8302930 0.8302930 1.0300007</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 0.4308777 1.2297083 -1.5593656 -0.1682452</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -1.3194635 -0.2327999 -0.7143765 -0.8965258 1.4065439 -0.7143765</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 0.8600960 -0.4735882 0.6779467 1.4065439</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 +214,38 @@
|
||||
<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 1 1 1 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 B 1 2 8 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 C 1 0.5 8 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 D 1 1 16 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 E 4 0.5 4 16</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 F 4 1 1 16</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 G 16 <=0.125 16 8</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 H 16 0.25 8 8</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 I 4 1 8 8</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 J 4 1 1 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 16 1 4 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 B 4 0.25 1 8</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 C >=32 0.125 4 <=0.5</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 D >=32 0.5 <=0.5 <=0.5</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 E 4 0.125 1 8</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 F 4 0.5 >=8 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 G <=1 0.5 1 8</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 H 16 1 2 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 I 16 0.0625 >=8 <=0.5</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 J 4 0.125 4 2</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] -0.55258772 -0.05081832 -0.65116115 -0.10941895 0.20887247 0.11308804</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 0.23423260 0.29283323 0.40187176 0.11308804</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.61790612 -0.10920284 -0.05949768 -0.23827191 -0.28797707 0.45880700</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] -0.23661482 0.29204478 -0.21259079 -0.22460280</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> 3 C 1 0.5 8 1 -0.65116115</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 A 1 1 1 4 -0.55258772</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 D 1 1 16 2 -0.10941895</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 B 1 2 8 2 -0.05081832</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 F 4 1 1 16 0.11308804</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 J 4 1 1 16 0.11308804</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 E 4 0.5 4 16 0.20887247</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 G 16 <=0.125 16 8 0.23423260</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 H 16 0.25 8 8 0.29283323</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 I 4 1 8 8 0.40187176</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 4 0.125 1 8 -0.28797707</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 D >=32 0.5 <=0.5 <=0.5 -0.23827191</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 G <=1 0.5 1 8 -0.23661482</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 J 4 0.125 4 2 -0.22460280</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 I 16 0.0625 >=8 <=0.5 -0.21259079</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 B 4 0.25 1 8 -0.10920284</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 C >=32 0.125 4 <=0.5 -0.05949768</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 H 16 1 2 1 0.29204478</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 F 4 0.5 >=8 4 0.45880700</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 A 16 1 4 2 0.61790612</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 +257,17 @@
|
||||
<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 1 0.5 8 1 -0.65116115 0.00000000</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 A 1 1 1 4 -0.55258772 0.09857343</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 D 1 1 16 2 -0.10941895 0.54174220</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 B 1 2 8 2 -0.05081832 0.60034283</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 F 4 1 1 16 0.11308804 0.76424920</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 J 4 1 1 16 0.11308804 0.76424920</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 E 4 0.5 4 16 0.20887247 0.86003362</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 G 16 <=0.125 16 8 0.23423260 0.88539375</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 H 16 0.25 8 8 0.29283323 0.94399438</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 I 4 1 8 8 0.40187176 1.05303291</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 0.125 4 <=0.5 -0.05949768 0.00000000</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 B 4 0.25 1 8 -0.10920284 0.04970516</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 I 16 0.0625 >=8 <=0.5 -0.21259079 0.15309311</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 J 4 0.125 4 2 -0.22460280 0.16510512</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 G <=1 0.5 1 8 -0.23661482 0.17711714</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 D >=32 0.5 <=0.5 <=0.5 -0.23827191 0.17877424</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 E 4 0.125 1 8 -0.28797707 0.22847939</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 H 16 1 2 1 0.29204478 0.35154246</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 F 4 0.5 >=8 4 0.45880700 0.51830468</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 A 16 1 4 2 0.61790612 0.67740380</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