P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2024-12-26 16:46:13 +01:00
Code Releases Activity
7d4de8eb35
AMR/reference/av_from_text.html
github-actions 7d4de8eb35 Built site for AMR: 1.8.2.9124@a4cd38c
2023-02-14 09:49:26 +00:00

255 lines
18 KiB
HTML
Raw Blame History

<!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="Use this function on e.g. clinical texts from health care records. It returns a list with all antiviral drugs, doses and forms of administration found in the texts."><title>Retrieve Antiviral Drug Names and Doses from Clinical Text — av_from_text • 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="Retrieve Antiviral Drug Names and Doses from Clinical Text — av_from_text"><meta property="og:description" content="Use this function on e.g. clinical texts from health care records. It returns a list with all antiviral drugs, doses and forms of administration found in the texts."><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="">1.8.2.9124</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">
<a class="nav-link" href="../index.html">
<span class="fa fa-home"></span>
Home
</a>
</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--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="../reference/AMR-options.html">
<span class="fa fa-gear"></span>
User- Or Team-specific Package Settings
</a>
<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>
Data Sets for Download / Own Use
</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/SPSS.html">
<span class="fa fa-file-upload"></span>
Import Data From SPSS/SAS/Stata
</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="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>
<li class="nav-item">
<a class="nav-link" href="../news/index.html">
<span class="far fa far fa-newspaper"></span>
Changelog
</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="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>Retrieve Antiviral Drug Names and Doses from Clinical Text</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/av_from_text.R" class="external-link"><code>R/av_from_text.R</code></a></small>
<div class="d-none name"><code>av_from_text.Rd</code></div>
</div>
<div class="ref-description section level2">
<p>Use this function on e.g. clinical texts from health care records. It returns a <a href="https://rdrr.io/r/base/list.html" class="external-link">list</a> with all antiviral drugs, doses and forms of administration found in the texts.</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">av_from_text</span><span class="op">(</span></span>
<span> <span class="va">text</span>,</span>
<span> type <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"drug"</span>, <span class="st">"dose"</span>, <span class="st">"administration"</span><span class="op">)</span>,</span>
<span> collapse <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span> translate_av <span class="op">=</span> <span class="cn">FALSE</span>,</span>
<span> thorough_search <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span> info <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/interactive.html" class="external-link">interactive</a></span><span class="op">(</span><span class="op">)</span>,</span>
<span> <span class="va">...</span></span>
<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>text</dt>
<dd><p>text to analyse</p></dd>
<dt>type</dt>
<dd><p>type of property to search for, either <code>"drug"</code>, <code>"dose"</code> or <code>"administration"</code>, see <em>Examples</em></p></dd>
<dt>collapse</dt>
<dd><p>a <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> to pass on to <code>paste(, collapse = ...)</code> to only return one <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> per element of <code>text</code>, see <em>Examples</em></p></dd>
<dt>translate_av</dt>
<dd><p>if <code>type = "drug"</code>: a column name of the <a href="antibiotics.html">antivirals</a> data set to translate the antibiotic abbreviations to, using <code><a href="av_property.html">av_property()</a></code>. Defaults to <code>FALSE</code>. Using <code>TRUE</code> is equal to using "name".</p></dd>
<dt>thorough_search</dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether the input must be extensively searched for misspelling and other faulty input values. Setting this to <code>TRUE</code> will take considerably more time than when using <code>FALSE</code>. At default, it will turn <code>TRUE</code> when all input elements contain a maximum of three words.</p></dd>
<dt>info</dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether a progress bar should be printed, defaults to <code>TRUE</code> only in interactive mode</p></dd>
<dt>...</dt>
<dd><p>arguments passed on to <code><a href="as.av.html">as.av()</a></code></p></dd>
</dl></div>
<div class="section level2">
<h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
<p>A <a href="https://rdrr.io/r/base/list.html" class="external-link">list</a>, or a <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> if <code>collapse</code> is not <code>NULL</code></p>
</div>
<div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
<p>This function is also internally used by <code><a href="as.av.html">as.av()</a></code>, although it then only searches for the first drug name and will throw a note if more drug names could have been returned. Note: the <code><a href="as.av.html">as.av()</a></code> function may use very long regular expression to match brand names of antiviral drugs. This may fail on some systems.</p><div class="section">
<h3 id="argument-type">Argument <code>type</code><a class="anchor" aria-label="anchor" href="#argument-type"></a></h3>
<p>At default, the function will search for antiviral drug names. All text elements will be searched for official names, ATC codes and brand names. As it uses <code><a href="as.av.html">as.av()</a></code> internally, it will correct for misspelling.</p>
<p>With <code>type = "dose"</code> (or similar, like "dosing", "doses"), all text elements will be searched for <a href="https://rdrr.io/r/base/numeric.html" class="external-link">numeric</a> values that are higher than 100 and do not resemble years. The output will be <a href="https://rdrr.io/r/base/numeric.html" class="external-link">numeric</a>. It supports any unit (g, mg, IE, etc.) and multiple values in one clinical text, see <em>Examples</em>.</p>
<p>With <code>type = "administration"</code> (or abbreviations, like "admin", "adm"), all text elements will be searched for a form of drug administration. It supports the following forms (including common abbreviations): buccal, implant, inhalation, instillation, intravenous, nasal, oral, parenteral, rectal, sublingual, transdermal and vaginal. Abbreviations for oral (such as 'po', 'per os') will become "oral", all values for intravenous (such as 'iv', 'intraven') will become "iv". It supports multiple values in one clinical text, see <em>Examples</em>.</p>
</div>
<div class="section">
<h3 id="argument-collapse">Argument <code>collapse</code><a class="anchor" aria-label="anchor" href="#argument-collapse"></a></h3>
<p>Without using <code>collapse</code>, this function will return a <a href="https://rdrr.io/r/base/list.html" class="external-link">list</a>. This can be convenient to use e.g. inside a <code><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate()</a></code>):<br><code>df %&gt;% mutate(avx = av_from_text(clinical_text))</code></p>
<p>The returned AV codes can be transformed to official names, groups, etc. with all <code><a href="av_property.html">av_*</a></code> functions such as <code><a href="av_property.html">av_name()</a></code> and <code><a href="av_property.html">av_group()</a></code>, or by using the <code>translate_av</code> argument.</p>
<p>With using <code>collapse</code>, this function will return a <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a>:<br><code>df %&gt;% mutate(avx = av_from_text(clinical_text, collapse = "|"))</code></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="fu">av_from_text</span><span class="op">(</span><span class="st">"28/03/2020 valaciclovir po tid"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [[1]]</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'av'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] VALA</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-in"><span><span class="fu">av_from_text</span><span class="op">(</span><span class="st">"28/03/2020 valaciclovir po tid"</span>, type <span class="op">=</span> <span class="st">"admin"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [[1]]</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "oral"</span>
<span class="r-out co"><span class="r-pr">#&gt;</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>
View Git Blame Copy Permalink