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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-0.4.5/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="">1.8.2.9099</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9100</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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@ -196,30 +196,31 @@
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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>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] R R R I S S R I R S</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] S I R I R S I I S S</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] -0.4743416 -0.4743416 1.8973666 -0.4743416 1.8973666 -0.4743416</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] -0.4743416 -0.4743416 -0.4743416 -0.4743416</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] 1 8 8 0.25 32 0.25 <=0.01 >=256 128 0.0625</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 2 0.5 32 0.025 <=0.005 <=0.005 1 0.01 0.025 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [10] 0.01 </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] -0.2344009 0.3848258 0.3848258 -0.6472187 0.7976436 -0.6472187</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] -1.6057520 1.4168703 1.2104614 -1.0600365</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 1.0124233 0.5545130 1.9282440 -0.4350148 -0.9666323 -0.9666323</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 0.7834682 -0.7376771 -0.4350148 -0.7376771</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] -0.2344009 0.3848258 0.3848258 -0.6472187 0.7976436 -0.6472187</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] -1.6057520 1.4168703 1.2104614 -1.0600365</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 1.0124233 0.5545130 1.9282440 -0.4350148 -0.9666323 -0.9666323</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 0.7834682 -0.7376771 -0.4350148 -0.7376771</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] 35 32 25 11 24 50 37 25 45 42</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 27 42 47 19 21 32 7 27 11 32</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] 0.20559684 -0.05139921 -0.65105665 -1.85037152 -0.73672199 1.49057706</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 0.37692753 -0.65105665 1.06225032 0.80525427</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.03968726 1.23030512 1.62717774 -0.59530893 -0.43655988 0.43655988</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] -1.54780321 0.03968726 -1.23030512 0.43655988</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>
|
||||
@ -230,35 +231,35 @@
|
||||
<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 23 4 >=16</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 B R 18 8 <=1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 C I 23 16 >=16</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 D R 27 4 >=16</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 E R 27 8 >=16</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 F S 29 4 8</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 G R 23 8 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 H R 26 1 <=1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 I I 26 2 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 J R 31 2 <=1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 A S 24 2 >=16</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 B I 31 4 >=16</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 C S 22 4 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 D R 18 1 0.5</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 E I 18 0.5 >=16</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 F S 25 1 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 G I 30 2 8</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 H I 25 0.5 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 I R 31 2 0.5</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 J I 19 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" and</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> "tobr"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -0.21933074 -0.41717151 0.19830380 0.53628817 0.74510544 0.05006051</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 0.19790396 -0.50063133 -0.63808424 0.04755593</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.2382463 0.7955297 -0.1157524 -0.2672839 -0.4858364 -0.4005406</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 0.4131124 -0.4981535 0.5828624 -0.2621839</span>
|
||||
<span class="r-in"><span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span> <span class="op"><-</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span>, <span class="fu">where</span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Calculating mean AMR distance based on columns "gent" and "tobr"</span>
|
||||
<span class="r-in"><span><span class="va">y</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/order.html" class="external-link">order</a></span><span class="op">(</span><span class="va">y</span><span class="op">$</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> 8 H R 26 1 <=1 -1.4835846</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 J R 31 2 <=1 -1.0659501</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 I I 26 2 2 -0.7902446</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 B R 18 8 <=1 -0.2306810</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 F S 29 4 8 0.1788009</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 G R 23 8 4 0.3207300</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 A S 23 4 >=16 0.4545064</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 D R 27 4 >=16 0.4545064</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 E R 27 8 >=16 0.8721410</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 C I 23 16 >=16 1.2897755</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 D R 18 1 0.5 -0.8682389</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 H I 25 0.5 2 -0.8274710</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 F S 25 1 1 -0.6322451</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 I R 31 2 0.5 -0.4370192</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 E I 18 0.5 >=16 -0.1194896</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 C S 22 4 1 0.2301943</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 J I 19 4 1 0.2301943</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 G I 30 2 8 0.5069560</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 A S 24 2 >=16 0.7429498</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 B I 31 4 >=16 1.1741694</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>
|
||||
@ -270,17 +271,17 @@
|
||||
<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 I 23 16 >=16 0.19830380 0.0000000000</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 G R 23 8 4 0.19790396 0.0003998324</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 F S 29 4 8 0.05006051 0.1482432883</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 J R 31 2 <=1 0.04755593 0.1507478663</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 D R 27 4 >=16 0.53628817 0.3379843756</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 A S 23 4 >=16 -0.21933074 0.4176345348</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 E R 27 8 >=16 0.74510544 0.5468016429</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 B R 18 8 <=1 -0.41717151 0.6154753058</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 H R 26 1 <=1 -0.50063133 0.6989351238</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 I I 26 2 2 -0.63808424 0.8363880331</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 S 22 4 1 -0.1157524 0.0000000</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 J I 19 4 1 -0.2621839 0.1464315</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 D R 18 1 0.5 -0.2672839 0.1515315</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 F S 25 1 1 -0.4005406 0.2847882</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 A S 24 2 >=16 0.2382463 0.3539987</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 E I 18 0.5 >=16 -0.4858364 0.3700839</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 H I 25 0.5 2 -0.4981535 0.3824011</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 G I 30 2 8 0.4131124 0.5288649</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 I R 31 2 0.5 0.5828624 0.6986148</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 B I 31 4 >=16 0.7955297 0.9112821</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