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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-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><link href="../deps/Fira_Code-0.4.6/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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<![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="">2.0.0.9013</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9014</small>
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@ -201,31 +201,30 @@
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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] R R S S I R S R S R</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] I I R I I I R S S R</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] -0.621059 -0.621059 1.449138 -0.621059 -0.621059 -0.621059 1.449138</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [8] -0.621059 -0.621059 1.449138</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] 0.005 0.25 >=256 <=0.002 1 <=0.002 0.5 1 128 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [10] 4 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.01 8 0.025 2 0.125 0.005 128 0.01 2 1 </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] -1.07476790 -0.13959336 1.51738462 -1.29380847 0.19180224 -1.29380847</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 0.02610444 0.19180224 1.35168682 0.52319783</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -1.0080431 0.9684558 -0.7371152 0.5585577 -0.2612383 -1.2129921</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 1.7882519 -1.0080431 0.5585577 0.3536087</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] -1.07476790 -0.13959336 1.51738462 -1.29380847 0.19180224 -1.29380847</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 0.02610444 0.19180224 1.35168682 0.52319783</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -1.0080431 0.9684558 -0.7371152 0.5585577 -0.2612383 -1.2129921</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 1.7882519 -1.0080431 0.5585577 0.3536087</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] 22 44 8 29 39 44 15 49 11 24</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 10 50 31 17 26 49 37 45 28 13</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] -0.43795351 1.04435068 -1.38123800 0.03368873 0.70746337 1.04435068</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] -0.90959576 1.38123800 -1.17910561 -0.30319859</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -1.41392483 1.33156027 0.02745485 -0.93346493 -0.31573079 1.26292315</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 0.43927762 0.98837464 -0.17845653 -1.20801344</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>
|
||||
@ -236,21 +235,21 @@
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||||
<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 S 20 2 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 B S 23 0.5 0.5</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 C I 25 0.5 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 D S 19 16 0.5</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 E I 24 1 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 F I 28 0.5 0.5</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 G R 31 4 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 H S 22 8 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 I S 21 0.5 0.5</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 J R 30 0.5 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 A S 19 >=16 <=1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 B R 20 8 <=1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 C I 20 2 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 D S 19 <=1 8</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 E I 23 4 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 F I 31 <=1 8</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 G R 18 2 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 H I 22 2 <=1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 I I 22 <=1 <=1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 J I 25 >=16 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> and "tobr"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -0.07375917 -0.63113176 -0.27390329 -0.21345353 0.03479741 -0.33098765</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 1.54821445 0.07224506 -0.75118940 0.61916787</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -0.1865874 0.3129310 -0.1974612 -0.2212515 0.1561783 0.5594410</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 0.2653504 -0.4668135 -0.6252799 0.4034927</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>
|
||||
@ -267,16 +266,16 @@
|
||||
<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 I 25 0.5 1 -0.27390329 0.00000000</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 F I 28 0.5 0.5 -0.33098765 0.05708436</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 D S 19 16 0.5 -0.21345353 0.06044977</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 A S 20 2 2 -0.07375917 0.20014413</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 E I 24 1 2 0.03479741 0.30870071</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 H S 22 8 1 0.07224506 0.34614835</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 B S 23 0.5 0.5 -0.63113176 0.35722847</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 I S 21 0.5 0.5 -0.75118940 0.47728611</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 J R 30 0.5 1 0.61916787 0.89307117</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 G R 31 4 4 1.54821445 1.82211774</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 C I 20 2 4 -0.1974612 0.00000000</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 A S 19 >=16 <=1 -0.1865874 0.01087383</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 D S 19 <=1 8 -0.2212515 0.02379027</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 H I 22 2 <=1 -0.4668135 0.26935231</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 E I 23 4 4 0.1561783 0.35363955</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 I I 22 <=1 <=1 -0.6252799 0.42781873</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 G R 18 2 4 0.2653504 0.46281164</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 B R 20 8 <=1 0.3129310 0.51039218</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 J I 25 >=16 2 0.4034927 0.60095395</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 F I 31 <=1 8 0.5594410 0.75690225</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