mirror of
https://github.com/msberends/AMR.git
synced 2025-07-27 21:25:29 +02:00
Built site for AMR: 1.8.2.9076@77d9cf1
This commit is contained in:
github-actions
@ -1,5 +1,5 @@
|
||||
<!DOCTYPE html>
|
||||
<!-- 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]>
|
||||
<!-- 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-0.4.4/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="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]>
|
||||
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
|
||||
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
|
||||
<![endif]--></head><body>
|
||||
@ -10,7 +10,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9074</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9076</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
@ -75,17 +75,17 @@
|
||||
<a class="dropdown-item" href="../reference/mo_property.html">
|
||||
<span class="fa fa-bug"></span>
|
||||
|
||||
Get properties of a microorganism
|
||||
Get taxonomy of a microorganism
|
||||
</a>
|
||||
<a class="dropdown-item" href="../reference/ab_property.html">
|
||||
<span class="fa fa-capsules"></span>
|
||||
|
||||
Get properties of an antibiotic
|
||||
Get properties of an antibiotic drug
|
||||
</a>
|
||||
<a class="dropdown-item" href="../reference/av_property.html">
|
||||
<span class="fa fa-capsules"></span>
|
||||
|
||||
Get properties of an antiviral agent
|
||||
Get properties of an antiviral drug
|
||||
</a>
|
||||
</div>
|
||||
</li>
|
||||
@ -127,28 +127,19 @@
|
||||
</nav><div class="container template-reference-topic">
|
||||
<div class="row">
|
||||
<main id="main" class="col-md-9"><div class="page-header">
|
||||
<img src="../logo.svg" class="logo" alt=""><h1>Mean AMR Distance</h1>
|
||||
<img src="../logo.svg" class="logo" alt=""><h1>Calculate the Mean AMR Distance</h1>
|
||||
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/mean_amr_distance.R" class="external-link"><code>R/mean_amr_distance.R</code></a></small>
|
||||
<div class="d-none name"><code>mean_amr_distance.Rd</code></div>
|
||||
</div>
|
||||
|
||||
<div class="ref-description section level2">
|
||||
<p>This function calculates a normalised mean for antimicrobial resistance between multiple observations.</p>
|
||||
<p>Calculates a normalised mean for antimicrobial resistance between multiple observations, to help to identify similar isolates without comparing antibiograms by hand.</p>
|
||||
</div>
|
||||
|
||||
<div class="section level2">
|
||||
<h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span>
|
||||
<span></span>
|
||||
<span><span class="co"># S3 method for default</span></span>
|
||||
<span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span>
|
||||
<span></span>
|
||||
<span><span class="co"># S3 method for mic</span></span>
|
||||
<span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span>
|
||||
<span></span>
|
||||
<span><span class="co"># S3 method for disk</span></span>
|
||||
<span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span>
|
||||
<span></span>
|
||||
<span><span class="co"># S3 method for rsi</span></span>
|
||||
<span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span>, combine_SI <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
|
||||
<span></span>
|
||||
@ -165,7 +156,7 @@
|
||||
|
||||
|
||||
<dt>...</dt>
|
||||
<dd><p>variables to select (supports tidy selection such as <code>column1:column4</code> and <code><a href="https://tidyselect.r-lib.org/reference/language.html" class="external-link">where(is.mic)</a></code>), and can thus also be <a href="antibiotic_class_selectors.html">antibiotic selectors</a></p></dd>
|
||||
<dd><p>variables to select (supports <a href="https://tidyselect.r-lib.org/reference/language.html" class="external-link">tidyselect language</a> such as <code>column1:column4</code> and <code>where(is.mic)</code>, and can thus also be <a href="antibiotic_class_selectors.html">antibiotic selectors</a></p></dd>
|
||||
|
||||
|
||||
<dt>combine_SI</dt>
|
||||
@ -200,11 +191,11 @@
|
||||
<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] 0.125 1 0.125 16 0.5 0.005 0.025 0.25 >=32 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [10] <=0.001</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.01 0.002 >=256 1 <=0.001 0.01 64 0.005 64 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [10] >=256 </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] -0.15089674 0.48954269 -0.15089674 1.34346192 0.27606288 -1.14226627</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] -0.64658150 0.06258307 1.55694173 -1.63795104</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -0.7233354 -1.0310806 1.2175417 0.1572324 -1.1636193 -0.7233354</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 0.9524644 -0.8558740 0.9524644 1.2175417</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>
|
||||
@ -215,37 +206,37 @@
|
||||
<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 8 2 <=1 <=1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 B <=2 2 16 <=1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 C >=16 >=4 2 <=1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 D >=16 0.125 2 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 E 4 >=4 <=1 8</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 F 4 >=4 8 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 G <=2 0.125 2 <=1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 H >=16 0.25 <=1 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 I >=16 0.25 8 8</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 J <=2 0.5 <=1 <=1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 A 8 1 2 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 B 32 >=4 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 16 >=4 2 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 E 4 >=4 1 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 F 16 1 4 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 G 4 0.5 1 >=8</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 H 4 0.25 1 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 I 16 0.5 1 0.5</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 J 8 0.125 >=8 0.5</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] -0.18987114 0.10887987 0.28105302 -0.11068834 0.34470481 0.44567516</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] -0.86673217 0.04090765 0.74321579 -0.79714465</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.0410109 0.8951387 -0.4091718 0.5415853 -0.1399200 0.6721245</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] -0.1964756 -0.6867320 -0.4492455 -0.2683146</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> 7 G <=2 0.125 2 <=1 -0.86673217</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 J <=2 0.5 <=1 <=1 -0.79714465</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 A 8 2 <=1 <=1 -0.18987114</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 D >=16 0.125 2 2 -0.11068834</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 H >=16 0.25 <=1 4 0.04090765</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 B <=2 2 16 <=1 0.10887987</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 C >=16 >=4 2 <=1 0.28105302</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 E 4 >=4 <=1 8 0.34470481</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 F 4 >=4 8 2 0.44567516</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 I >=16 0.25 8 8 0.74321579</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 H 4 0.25 1 2 -0.6867320</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 I 16 0.5 1 0.5 -0.4492455</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 C 4 0.25 4 1 -0.4091718</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 J 8 0.125 >=8 0.5 -0.2683146</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 G 4 0.5 1 >=8 -0.1964756</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 E 4 >=4 1 2 -0.1399200</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 A 8 1 2 2 0.0410109</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 D 16 >=4 2 2 0.5415853</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 F 16 1 4 4 0.6721245</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 B 32 >=4 1 >=8 0.8951387</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>
|
||||
@ -258,16 +249,16 @@
|
||||
<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 >=4 2 <=1 0.28105302 0.00000000</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 E 4 >=4 <=1 8 0.34470481 0.06365179</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 F 4 >=4 8 2 0.44567516 0.16462214</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 B <=2 2 16 <=1 0.10887987 0.17217315</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 H >=16 0.25 <=1 4 0.04090765 0.24014537</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 D >=16 0.125 2 2 -0.11068834 0.39174136</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 I >=16 0.25 8 8 0.74321579 0.46216277</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 A 8 2 <=1 <=1 -0.18987114 0.47092416</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 J <=2 0.5 <=1 <=1 -0.79714465 1.07819767</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 G <=2 0.125 2 <=1 -0.86673217 1.14778519</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 C 4 0.25 4 1 -0.4091718 0.0000000</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 I 16 0.5 1 0.5 -0.4492455 0.0400737</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 J 8 0.125 >=8 0.5 -0.2683146 0.1408572</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 G 4 0.5 1 >=8 -0.1964756 0.2126962</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 E 4 >=4 1 2 -0.1399200 0.2692518</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 H 4 0.25 1 2 -0.6867320 0.2775602</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 A 8 1 2 2 0.0410109 0.4501827</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 D 16 >=4 2 2 0.5415853 0.9507571</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 F 16 1 4 4 0.6721245 1.0812963</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 B 32 >=4 1 >=8 0.8951387 1.3043105</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