mirror of https://github.com/msberends/AMR.git
346 lines
33 KiB
HTML
346 lines
33 KiB
HTML
<!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="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-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.8/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.8/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>
|
||
<a href="#main" class="visually-hidden-focusable">Skip to contents</a>
|
||
|
||
|
||
<nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary"><div class="container">
|
||
|
||
<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="">2.1.1.9013</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">
|
||
<span class="navbar-toggler-icon"></span>
|
||
</button>
|
||
|
||
<div id="navbar" class="collapse navbar-collapse ms-3">
|
||
<ul class="navbar-nav me-auto"><li class="nav-item dropdown">
|
||
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--how-to">
|
||
<span class="fa fa-question-circle"></span>
|
||
|
||
How to
|
||
</a>
|
||
<div class="dropdown-menu" aria-labelledby="dropdown--how-to">
|
||
<a class="dropdown-item" href="../articles/AMR.html">
|
||
<span class="fa fa-directions"></span>
|
||
|
||
Conduct AMR Analysis
|
||
</a>
|
||
<a class="dropdown-item" href="../reference/antibiogram.html">
|
||
<span class="fa fa-file-prescription"></span>
|
||
|
||
Generate Antibiogram (Trad./Syndromic/WISCA)
|
||
</a>
|
||
<a class="dropdown-item" href="../articles/resistance_predict.html">
|
||
<span class="fa fa-dice"></span>
|
||
|
||
Predict Antimicrobial Resistance
|
||
</a>
|
||
<a class="dropdown-item" href="../articles/datasets.html">
|
||
<span class="fa fa-database"></span>
|
||
|
||
Download Data Sets for Own Use
|
||
</a>
|
||
<a class="dropdown-item" href="../reference/AMR-options.html">
|
||
<span class="fa fa-gear"></span>
|
||
|
||
Set User- Or Team-specific Package Settings
|
||
</a>
|
||
<a class="dropdown-item" href="../articles/PCA.html">
|
||
<span class="fa fa-compress"></span>
|
||
|
||
Conduct Principal Component Analysis for AMR
|
||
</a>
|
||
<a class="dropdown-item" href="../articles/MDR.html">
|
||
<span class="fa fa-skull-crossbones"></span>
|
||
|
||
Determine Multi-Drug Resistance (MDR)
|
||
</a>
|
||
<a class="dropdown-item" href="../articles/WHONET.html">
|
||
<span class="fa fa-globe-americas"></span>
|
||
|
||
Work with WHONET Data
|
||
</a>
|
||
<a class="dropdown-item" href="../articles/EUCAST.html">
|
||
<span class="fa fa-exchange-alt"></span>
|
||
|
||
Apply Eucast Rules
|
||
</a>
|
||
<a class="dropdown-item" href="../reference/mo_property.html">
|
||
<span class="fa fa-bug"></span>
|
||
|
||
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 Drug
|
||
</a>
|
||
<a class="dropdown-item" href="../reference/av_property.html">
|
||
<span class="fa fa-capsules"></span>
|
||
|
||
Get Properties of an Antiviral Drug
|
||
</a>
|
||
</div>
|
||
</li>
|
||
<li class="nav-item dropdown">
|
||
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
|
||
<span class="fa fa-layer-group"></span>
|
||
|
||
With other pkgs
|
||
</a>
|
||
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
|
||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||
<span class="fa fa-layer-group"></span>
|
||
|
||
AMR & dplyr/tidyverse
|
||
</a>
|
||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||
<span class="fa fa-layer-group"></span>
|
||
|
||
AMR & data.table
|
||
</a>
|
||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||
<span class="fa fa-layer-group"></span>
|
||
|
||
AMR & tidymodels
|
||
</a>
|
||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||
<span class="fa fa-layer-group"></span>
|
||
|
||
AMR & base R
|
||
</a>
|
||
</div>
|
||
</li>
|
||
<li class="active nav-item">
|
||
<a class="nav-link" href="../reference/index.html">
|
||
<span class="fa fa-book-open"></span>
|
||
|
||
Manual
|
||
</a>
|
||
</li>
|
||
<li class="nav-item">
|
||
<a class="nav-link" href="../authors.html">
|
||
<span class="fa fa-users"></span>
|
||
|
||
Authors
|
||
</a>
|
||
</li>
|
||
</ul><form class="form-inline my-2 my-lg-0" role="search">
|
||
<input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
|
||
|
||
<ul class="navbar-nav"><li class="nav-item">
|
||
<a class="nav-link" href="../news/index.html">
|
||
<span class="far fa far fa-newspaper"></span>
|
||
|
||
Changelog
|
||
</a>
|
||
</li>
|
||
<li class="nav-item">
|
||
<a class="external-link nav-link" href="https://github.com/msberends/AMR">
|
||
<span class="fab fa fab fa-github"></span>
|
||
|
||
Source Code
|
||
</a>
|
||
</li>
|
||
</ul></div>
|
||
|
||
|
||
</div>
|
||
</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>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>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 sir</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>
|
||
<span><span class="co"># S3 method for data.frame</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>
|
||
<span><span class="fu">amr_distance_from_row</span><span class="op">(</span><span class="va">amr_distance</span>, <span class="va">row</span><span class="op">)</span></span></code></pre></div>
|
||
</div>
|
||
|
||
<div class="section level2">
|
||
<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
|
||
<dl><dt>x</dt>
|
||
<dd><p>a vector of class <a href="as.sir.html">sir</a>, <a href="as.mic.html">mic</a> or <a href="as.disk.html">disk</a>, or a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> containing columns of any of these classes</p></dd>
|
||
|
||
|
||
<dt>...</dt>
|
||
<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>
|
||
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether all values of S and I must be merged into one, so the input only consists of S+I vs. R (susceptible vs. resistant) - the default is <code>TRUE</code></p></dd>
|
||
|
||
|
||
<dt>amr_distance</dt>
|
||
<dd><p>the outcome of <code>mean_amr_distance()</code></p></dd>
|
||
|
||
|
||
<dt>row</dt>
|
||
<dd><p>an index, such as a row number</p></dd>
|
||
|
||
</dl></div>
|
||
<div class="section level2">
|
||
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
|
||
<p>The mean AMR distance is effectively <a href="https://en.wikipedia.org/wiki/Standard_score" class="external-link">the Z-score</a>; a normalised numeric value to compare AMR test results which can help to identify similar isolates, without comparing antibiograms by hand.</p>
|
||
<p>MIC values (see <code><a href="as.mic.html">as.mic()</a></code>) are transformed with <code><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2()</a></code> first; their distance is thus calculated as <code>(log2(x) - mean(log2(x))) / sd(log2(x))</code>.</p>
|
||
<p>SIR values (see <code><a href="as.sir.html">as.sir()</a></code>) are transformed using <code>"S"</code> = 1, <code>"I"</code> = 2, and <code>"R"</code> = 3. If <code>combine_SI</code> is <code>TRUE</code> (default), the <code>"I"</code> will be considered to be 1.</p>
|
||
<p>For data sets, the mean AMR distance will be calculated per column, after which the mean per row will be returned, see <em>Examples</em>.</p>
|
||
<p>Use <code>amr_distance_from_row()</code> to subtract distances from the distance of one row, see <em>Examples</em>.</p>
|
||
</div>
|
||
<div class="section level2">
|
||
<h2 id="interpretation">Interpretation<a class="anchor" aria-label="anchor" href="#interpretation"></a></h2>
|
||
|
||
|
||
<p>Isolates with distances less than 0.01 difference from each other should be considered similar. Differences lower than 0.025 should be considered suspicious.</p>
|
||
</div>
|
||
|
||
<div class="section level2">
|
||
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
|
||
<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>
|
||
<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 S I I S I I R I</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] 1.449138 1.449138 -0.621059 -0.621059 -0.621059 -0.621059 -0.621059</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [8] -0.621059 1.449138 -0.621059</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] 0.002 0.5 0.125 128 0.25 0.5 256 0.125 0.125 64 </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] -1.6429088 -0.1673475 -0.5378223 1.3145519 -0.3525849 -0.1673475</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [7] 1.4997893 -0.5378223 -0.5378223 1.1293145</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] -1.6429088 -0.1673475 -0.5378223 1.3145519 -0.3525849 -0.1673475</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [7] 1.4997893 -0.5378223 -0.5378223 1.1293145</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] 40 45 43 14 42 40 37 15 42 11</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] 0.5182957 0.8832927 0.7372939 -1.3796886 0.6642945 0.5182957</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [7] 0.2992975 -1.3066892 0.6642945 -1.5986868</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>
|
||
<span class="r-in"><span> amox <span class="op">=</span> <span class="fu"><a href="random.html">random_sir</a></span><span class="op">(</span><span class="fl">10</span>, ab <span class="op">=</span> <span class="st">"amox"</span>, mo <span class="op">=</span> <span class="st">"Escherichia coli"</span><span class="op">)</span>,</span></span>
|
||
<span class="r-in"><span> cipr <span class="op">=</span> <span class="fu"><a href="random.html">random_disk</a></span><span class="op">(</span><span class="fl">10</span>, ab <span class="op">=</span> <span class="st">"cipr"</span>, mo <span class="op">=</span> <span class="st">"Escherichia coli"</span><span class="op">)</span>,</span></span>
|
||
<span class="r-in"><span> gent <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">"gent"</span>, mo <span class="op">=</span> <span class="st">"Escherichia coli"</span><span class="op">)</span>,</span></span>
|
||
<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 R 17 <=0.5 >=8</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> 2 B I 26 <=0.5 4</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> 3 C R 18 4 >=8</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> 4 D R 22 <=0.5 <=0.5</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> 5 E I 30 <=0.5 1</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> 6 F S 18 4 2</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> 7 G I 26 8 2</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> 8 H S 29 8 1</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> 9 I I 22 16 1</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> 10 J S 31 1 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> and "tobr"</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.12957466 -0.14083442 0.55230568 -0.36152662 -0.31478853 -0.33012168</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [7] 0.17672648 0.13748045 -0.07163669 0.22282068</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>
|
||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in order(y$amr_distance):</span> argument 1 is not a vector</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>
|
||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span></span></span>
|
||
<span class="r-in"><span> amr_distance <span class="op">=</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-in"><span> check_id_C <span class="op">=</span> <span class="fu">amr_distance_from_row</span><span class="op">(</span><span class="va">amr_distance</span>, <span class="va">id</span> <span class="op">==</span> <span class="st">"C"</span><span class="op">)</span></span></span>
|
||
<span class="r-in"><span> <span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/arrange.html" class="external-link">arrange</a></span><span class="op">(</span><span class="va">check_id_C</span><span class="op">)</span></span></span>
|
||
<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",</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 R 18 4 >=8 0.55230568 0.0000000</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> 2 J S 31 1 4 0.22282068 0.3294850</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> 3 G I 26 8 2 0.17672648 0.3755792</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> 4 H S 29 8 1 0.13748045 0.4148252</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> 5 A R 17 <=0.5 >=8 0.12957466 0.4227310</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> 6 I I 22 16 1 -0.07163669 0.6239424</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> 7 B I 26 <=0.5 4 -0.14083442 0.6931401</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> 8 E I 30 <=0.5 1 -0.31478853 0.8670942</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> 9 F S 18 4 2 -0.33012168 0.8824274</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> 10 D R 22 <=0.5 <=0.5 -0.36152662 0.9138323</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>
|
||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu"><a href="mo_property.html">mo_genus</a></span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"Enterococcus"</span> <span class="op">&</span> <span class="fu"><a href="mo_property.html">mo_species</a></span><span class="op">(</span><span class="op">)</span> <span class="op">!=</span> <span class="st">""</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">mo</span>, <span class="va">TCY</span>, <span class="fu"><a href="antibiotic_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>dist <span class="op">=</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">.</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/arrange.html" class="external-link">arrange</a></span><span class="op">(</span><span class="va">mo</span>, <span class="va">dist</span><span class="op">)</span></span></span>
|
||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Using column 'mo' as input for mo_genus()</span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Using column 'mo' as input for mo_species()</span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem)</span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Calculating mean AMR distance based on columns "TCY", "IPM", and "MEM"</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 63 × 5</span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Groups: mo [4]</span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> mo TCY IPM MEM dist</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><dbl></span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> B_ENTRC_AVIM S S NA 0 </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> B_ENTRC_AVIM S S NA 0 </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> B_ENTRC_CSSL NA S NA <span style="color: #BB0000;">NA</span> </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> B_ENTRC_FACM S S NA -<span style="color: #BB0000;">2.66</span> </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> B_ENTRC_FACM S R R -<span style="color: #BB0000;">0.423</span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> B_ENTRC_FACM S R R -<span style="color: #BB0000;">0.423</span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> B_ENTRC_FACM NA R R 0.224</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> B_ENTRC_FACM NA R R 0.224</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> B_ENTRC_FACM NA R R 0.224</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> B_ENTRC_FACM NA R R 0.224</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 53 more rows</span></span>
|
||
</code></pre></div>
|
||
</div>
|
||
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
|
||
</nav></aside></div>
|
||
|
||
|
||
<footer><div class="pkgdown-footer-left">
|
||
<p></p><p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p>
|
||
</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: 150px;"></a><a target="_blank" href="https://www.umcg.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/logos/logo_umcg.svg" style="max-width: 150px;"></a></p>
|
||
</div>
|
||
|
||
</footer></div>
|
||
|
||
|
||
|
||
|
||
|
||
</body></html>
|
||
|