mirror of
https://github.com/msberends/AMR.git
synced 2024-12-28 01:26:13 +01:00
337 lines
26 KiB
HTML
337 lines
26 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="With add_custom_antimicrobials() you can add your own custom antimicrobial drug names and codes."><title>Add Custom Antimicrobials — add_custom_antimicrobials • 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-0.4.9/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.9/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/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></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="Add Custom Antimicrobials — add_custom_antimicrobials"><meta property="og:description" content="With add_custom_antimicrobials() you can add your own custom antimicrobial drug names and codes."><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" data-bs-theme="dark"><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="">2.1.1.9022</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>Add Custom Antimicrobials</h1>
|
||
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/custom_antimicrobials.R" class="external-link"><code>R/custom_antimicrobials.R</code></a></small>
|
||
<div class="d-none name"><code>add_custom_antimicrobials.Rd</code></div>
|
||
</div>
|
||
|
||
<div class="ref-description section level2">
|
||
<p>With <code>add_custom_antimicrobials()</code> you can add your own custom antimicrobial drug names and codes.</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">add_custom_antimicrobials</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span>
|
||
<span></span>
|
||
<span><span class="fu">clear_custom_antimicrobials</span><span class="op">(</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 <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> resembling the <a href="antibiotics.html">antibiotics</a> data set, at least containing columns "ab" and "name"</p></dd>
|
||
|
||
</dl></div>
|
||
<div class="section level2">
|
||
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
|
||
<p><strong>Important:</strong> Due to how <span style="R">R</span> works, the <code>add_custom_antimicrobials()</code> function has to be run in every <span style="R">R</span> session - added antimicrobials are not stored between sessions and are thus lost when <span style="R">R</span> is exited.</p>
|
||
<p>There are two ways to circumvent this and automate the process of adding antimicrobials:</p>
|
||
<p><strong>Method 1:</strong> Using the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_custom_ab</a></code>, which is the preferred method. To use this method:</p><ol><li><p>Create a data set in the structure of the <a href="antibiotics.html">antibiotics</a> data set (containing at the very least columns "ab" and "name") and save it with <code><a href="https://rdrr.io/r/base/readRDS.html" class="external-link">saveRDS()</a></code> to a location of choice, e.g. <code>"~/my_custom_ab.rds"</code>, or any remote location.</p></li>
|
||
<li><p>Set the file location to the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_custom_ab</a></code>: <code>options(AMR_custom_ab = "~/my_custom_ab.rds")</code>. This can even be a remote file location, such as an https URL. Since options are not saved between <span style="R">R</span> sessions, it is best to save this option to the <code>.Rprofile</code> file so that it will be loaded on start-up of <span style="R">R</span>. To do this, open the <code>.Rprofile</code> file using e.g. <code>utils::file.edit("~/.Rprofile")</code>, add this text and save the file:</p>
|
||
<p></p><div class="sourceCode r"><pre><code><span><span class="co"># Add custom antimicrobial codes:</span></span>
|
||
<span><span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">options</a></span><span class="op">(</span>AMR_custom_ab <span class="op">=</span> <span class="st">"~/my_custom_ab.rds"</span><span class="op">)</span></span></code></pre><p></p></div>
|
||
<p>Upon package load, this file will be loaded and run through the <code>add_custom_antimicrobials()</code> function.</p></li>
|
||
</ol><p><strong>Method 2:</strong> Loading the antimicrobial additions directly from your <code>.Rprofile</code> file. Note that the definitions will be stored in a user-specific <span style="R">R</span> file, which is a suboptimal workflow. To use this method:</p><ol><li><p>Edit the <code>.Rprofile</code> file using e.g. <code>utils::file.edit("~/.Rprofile")</code>.</p></li>
|
||
<li><p>Add a text like below and save the file:</p>
|
||
<p></p><div class="sourceCode r"><pre><code><span> <span class="co"># Add custom antibiotic drug codes:</span></span>
|
||
<span> <span class="fu">AMR</span><span class="fu">::</span><span class="fu"><a href="../reference/add_custom_antimicrobials.html">add_custom_antimicrobials</a></span><span class="op">(</span></span>
|
||
<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>ab <span class="op">=</span> <span class="st">"TESTAB"</span>,</span>
|
||
<span> name <span class="op">=</span> <span class="st">"Test Antibiotic"</span>,</span>
|
||
<span> group <span class="op">=</span> <span class="st">"Test Group"</span><span class="op">)</span></span>
|
||
<span> <span class="op">)</span></span></code></pre><p></p></div></li>
|
||
</ol><p>Use <code>clear_custom_antimicrobials()</code> to clear the previously added antimicrobials.</p>
|
||
</div>
|
||
<div class="section level2">
|
||
<h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
|
||
<div class="dont-index"><p><code><a href="add_custom_microorganisms.html">add_custom_microorganisms()</a></code> to add custom microorganisms.</p></div>
|
||
</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="co"># \donttest{</span></span></span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span><span class="co"># returns NA and throws a warning (which is suppressed here):</span></span></span>
|
||
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/warning.html" class="external-link">suppressWarnings</a></span><span class="op">(</span></span></span>
|
||
<span class="r-in"><span> <span class="fu"><a href="as.ab.html">as.ab</a></span><span class="op">(</span><span class="st">"testab"</span><span class="op">)</span></span></span>
|
||
<span class="r-in"><span><span class="op">)</span></span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> Class 'ab'</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [1] <NA></span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span><span class="co"># now add a custom entry - it will be considered by as.ab() and</span></span></span>
|
||
<span class="r-in"><span><span class="co"># all ab_*() functions</span></span></span>
|
||
<span class="r-in"><span><span class="fu">add_custom_antimicrobials</span><span class="op">(</span></span></span>
|
||
<span class="r-in"><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> ab <span class="op">=</span> <span class="st">"TESTAB"</span>,</span></span>
|
||
<span class="r-in"><span> name <span class="op">=</span> <span class="st">"Test Antibiotic"</span>,</span></span>
|
||
<span class="r-in"><span> <span class="co"># you can add any property present in the</span></span></span>
|
||
<span class="r-in"><span> <span class="co"># 'antibiotics' data set, such as 'group':</span></span></span>
|
||
<span class="r-in"><span> group <span class="op">=</span> <span class="st">"Test Group"</span></span></span>
|
||
<span class="r-in"><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 Added one record to the internal antibiotics data set.</span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span><span class="co"># "testab" is now a new antibiotic:</span></span></span>
|
||
<span class="r-in"><span><span class="fu"><a href="as.ab.html">as.ab</a></span><span class="op">(</span><span class="st">"testab"</span><span class="op">)</span></span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> Class 'ab'</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [1] TESTAB</span>
|
||
<span class="r-in"><span><span class="fu"><a href="ab_property.html">ab_name</a></span><span class="op">(</span><span class="st">"testab"</span><span class="op">)</span></span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [1] "Test Antibiotic"</span>
|
||
<span class="r-in"><span><span class="fu"><a href="ab_property.html">ab_group</a></span><span class="op">(</span><span class="st">"testab"</span><span class="op">)</span></span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [1] "Test Group"</span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span><span class="fu"><a href="ab_property.html">ab_info</a></span><span class="op">(</span><span class="st">"testab"</span><span class="op">)</span></span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> $ab</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [1] "TESTAB"</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> $cid</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [1] NA</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> $name</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [1] "Test Antibiotic"</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> $group</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [1] "Test Group"</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> $atc</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [1] NA</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> $atc_group1</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [1] NA</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> $atc_group2</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [1] NA</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> $tradenames</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [1] NA</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> $loinc</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [1] NA</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> $ddd</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> $ddd$oral</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> $ddd$oral$amount</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [1] NA</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> $ddd$oral$units</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [1] NA</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> $ddd$iv</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> $ddd$iv$amount</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [1] NA</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> $ddd$iv$units</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [1] NA</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span><span class="co"># Add Co-fluampicil, which is one of the many J01CR50 codes, see</span></span></span>
|
||
<span class="r-in"><span><span class="co"># https://atcddd.fhi.no/ddd/list_of_ddds_combined_products/</span></span></span>
|
||
<span class="r-in"><span><span class="fu">add_custom_antimicrobials</span><span class="op">(</span></span></span>
|
||
<span class="r-in"><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> ab <span class="op">=</span> <span class="st">"COFLU"</span>,</span></span>
|
||
<span class="r-in"><span> name <span class="op">=</span> <span class="st">"Co-fluampicil"</span>,</span></span>
|
||
<span class="r-in"><span> atc <span class="op">=</span> <span class="st">"J01CR50"</span>,</span></span>
|
||
<span class="r-in"><span> group <span class="op">=</span> <span class="st">"Beta-lactams/penicillins"</span></span></span>
|
||
<span class="r-in"><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 Added one record to the internal antibiotics data set.</span>
|
||
<span class="r-in"><span><span class="fu"><a href="ab_property.html">ab_atc</a></span><span class="op">(</span><span class="st">"Co-fluampicil"</span><span class="op">)</span></span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [1] "J01CR50"</span>
|
||
<span class="r-in"><span><span class="fu"><a href="ab_property.html">ab_name</a></span><span class="op">(</span><span class="st">"J01CR50"</span><span class="op">)</span></span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [1] "Co-fluampicil"</span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span><span class="co"># even antibiotic selectors work</span></span></span>
|
||
<span class="r-in"><span><span class="va">x</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> random_column <span class="op">=</span> <span class="st">"some value"</span>,</span></span>
|
||
<span class="r-in"><span> coflu <span class="op">=</span> <span class="fu"><a href="as.sir.html">as.sir</a></span><span class="op">(</span><span class="st">"S"</span><span class="op">)</span>,</span></span>
|
||
<span class="r-in"><span> ampicillin <span class="op">=</span> <span class="fu"><a href="as.sir.html">as.sir</a></span><span class="op">(</span><span class="st">"R"</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">x</span></span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> random_column coflu ampicillin</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> 1 some value S R</span>
|
||
<span class="r-in"><span><span class="va">x</span><span class="op">[</span>, <span class="fu"><a href="antibiotic_class_selectors.html">betalactams</a></span><span class="op">(</span><span class="op">)</span><span class="op">]</span></span></span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> ℹ For betalactams() using columns 'coflu' (co-fluampicil) and</span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> 'ampicillin'</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> coflu ampicillin</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> 1 S R</span>
|
||
<span class="r-in"><span><span class="co"># }</span></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><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><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>
|
||
|