P281424
/
AMR
mirror of https://github.com/msberends/AMR.git
1
0
Fork 0
Code Releases Activity
AMR/reference/italicise_taxonomy.html

221 lines
15 KiB
HTML
Raw Normal View History

Built site for AMR: 1.8.1.9020@d6676e9
2022-08-21 16:59:35 +02:00
<!DOCTYPE html>
Built site for AMR: 2.1.0.9001@7dc9679
2023-07-20 08:32:45 +02:00
<!-- 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="According to the binomial nomenclature, the lowest four taxonomic levels (family, genus, species, subspecies) should be printed in italics. This function finds taxonomic names within strings and makes them italic."><title>Italicise Taxonomic Families, Genera, Species, Subspecies — italicise_taxonomy • 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-0.4.7/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="Italicise Taxonomic Families, Genera, Species, Subspecies — italicise_taxonomy"><meta property="og:description" content="According to the binomial nomenclature, the lowest four taxonomic levels (family, genus, species, subspecies) should be printed in italics. This function finds taxonomic names within strings and makes them italic."><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"><meta name="twi
Built site for AMR: 1.8.1.9020@d6676e9
2022-08-21 16:59:35 +02:00
<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>
Built site for AMR: 2.1.1@4c11a7b
2023-10-22 15:59:03 +02:00
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
Built site for AMR: 1.8.1.9020@d6676e9
2022-08-21 16:59:35 +02:00
<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">
Built site for AMR: 2.0.0.9019@0bcf55d
2023-05-24 16:03:18 +02:00
<ul class="navbar-nav me-auto"><li class="nav-item dropdown">
Built site for AMR: 1.8.1.9020@d6676e9
2022-08-21 16:59:35 +02:00
<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>
Built site for AMR: 1.8.2.9099@eef0006
2023-01-23 20:14:37 +01:00
Conduct AMR Analysis
Built site for AMR: 1.8.1.9020@d6676e9
2022-08-21 16:59:35 +02:00
</a>
Built site for AMR: 1.8.2.9111@aa48c6b
2023-02-08 17:01:47 +01:00
<a class="dropdown-item" href="../reference/antibiogram.html">
<span class="fa fa-file-prescription"></span>
Generate Antibiogram (Trad./Syndromic/WISCA)
</a>
Built site for AMR: 1.8.1.9020@d6676e9
2022-08-21 16:59:35 +02:00
<a class="dropdown-item" href="../articles/resistance_predict.html">
<span class="fa fa-dice"></span>
Built site for AMR: 1.8.2.9099@eef0006
2023-01-23 20:14:37 +01:00
Predict Antimicrobial Resistance
Built site for AMR: 1.8.1.9020@d6676e9
2022-08-21 16:59:35 +02:00
</a>
<a class="dropdown-item" href="../articles/datasets.html">
<span class="fa fa-database"></span>
Built site for AMR: 1.8.2.9147@4416394
2023-02-26 21:34:01 +01:00
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
Built site for AMR: 1.8.1.9020@d6676e9
2022-08-21 16:59:35 +02:00
</a>
<a class="dropdown-item" href="../articles/PCA.html">
<span class="fa fa-compress"></span>
Built site for AMR: 1.8.2.9099@eef0006
2023-01-23 20:14:37 +01:00
Conduct Principal Component Analysis for AMR
Built site for AMR: 1.8.1.9020@d6676e9
2022-08-21 16:59:35 +02:00
</a>
<a class="dropdown-item" href="../articles/MDR.html">
<span class="fa fa-skull-crossbones"></span>
Built site for AMR: 1.8.2.9099@eef0006
2023-01-23 20:14:37 +01:00
Determine Multi-Drug Resistance (MDR)
Built site for AMR: 1.8.1.9020@d6676e9
2022-08-21 16:59:35 +02:00
</a>
<a class="dropdown-item" href="../articles/WHONET.html">
<span class="fa fa-globe-americas"></span>
Built site for AMR: 1.8.2.9099@eef0006
2023-01-23 20:14:37 +01:00
Work with WHONET Data
Built site for AMR: 1.8.1.9020@d6676e9
2022-08-21 16:59:35 +02:00
</a>
<a class="dropdown-item" href="../articles/EUCAST.html">
<span class="fa fa-exchange-alt"></span>
Built site for AMR: 1.8.2.9099@eef0006
2023-01-23 20:14:37 +01:00
Apply Eucast Rules
Built site for AMR: 1.8.1.9020@d6676e9
2022-08-21 16:59:35 +02:00
</a>
<a class="dropdown-item" href="../reference/mo_property.html">
<span class="fa fa-bug"></span>
Built site for AMR: 1.8.2.9099@eef0006
2023-01-23 20:14:37 +01:00
Get Taxonomy of a Microorganism
Built site for AMR: 1.8.1.9020@d6676e9
2022-08-21 16:59:35 +02:00
</a>
<a class="dropdown-item" href="../reference/ab_property.html">
<span class="fa fa-capsules"></span>
Built site for AMR: 1.8.2.9099@eef0006
2023-01-23 20:14:37 +01:00
Get Properties of an Antibiotic Drug
Built site for AMR: 1.8.1.9020@d6676e9
2022-08-21 16:59:35 +02:00
</a>
Built site for AMR: 1.8.2.9049@496c08d
2022-11-13 08:54:32 +01:00
<a class="dropdown-item" href="../reference/av_property.html">
<span class="fa fa-capsules"></span>
Built site for AMR: 1.8.2.9099@eef0006
2023-01-23 20:14:37 +01:00
Get Properties of an Antiviral Drug
Built site for AMR: 1.8.2.9049@496c08d
2022-11-13 08:54:32 +01:00
</a>
Built site for AMR: 1.8.1.9020@d6676e9
2022-08-21 16:59:35 +02:00
</div>
</li>
Built site for AMR: 2.0.0.9019@0bcf55d
2023-05-24 16:03:18 +02:00
<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">
Built site for AMR: 2.0.0.9023@9591688
2023-05-27 10:53:23 +02:00
<span class="fa fa-layer-group"></span>
Built site for AMR: 2.0.0.9019@0bcf55d
2023-05-24 16:03:18 +02:00
With other pkgs
</a>
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
<a class="dropdown-item" href="../articles/other_pkg.html">
Built site for AMR: 2.0.0.9023@9591688
2023-05-27 10:53:23 +02:00
<span class="fa fa-layer-group"></span>
Built site for AMR: 2.0.0.9019@0bcf55d
2023-05-24 16:03:18 +02:00
AMR &amp; dplyr/tidyverse
</a>
<a class="dropdown-item" href="../articles/other_pkg.html">
Built site for AMR: 2.0.0.9023@9591688
2023-05-27 10:53:23 +02:00
<span class="fa fa-layer-group"></span>
Built site for AMR: 2.0.0.9019@0bcf55d
2023-05-24 16:03:18 +02:00
AMR &amp; data.table
</a>
<a class="dropdown-item" href="../articles/other_pkg.html">
Built site for AMR: 2.0.0.9023@9591688
2023-05-27 10:53:23 +02:00
<span class="fa fa-layer-group"></span>
Built site for AMR: 2.0.0.9019@0bcf55d
2023-05-24 16:03:18 +02:00
AMR &amp; tidymodels
</a>
<a class="dropdown-item" href="../articles/other_pkg.html">
Built site for AMR: 2.0.0.9023@9591688
2023-05-27 10:53:23 +02:00
<span class="fa fa-layer-group"></span>
Built site for AMR: 2.0.0.9019@0bcf55d
2023-05-24 16:03:18 +02:00
AMR &amp; base R
</a>
</div>
</li>
Built site for AMR: 1.8.1.9020@d6676e9
2022-08-21 16:59:35 +02:00
<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>
Built site for AMR: 2.0.0.9019@0bcf55d
2023-05-24 16:03:18 +02:00
</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">
Built site for AMR: 1.8.1.9020@d6676e9
2022-08-21 16:59:35 +02:00
<a class="nav-link" href="../news/index.html">
<span class="far fa far fa-newspaper"></span>
Changelog
</a>
</li>
Built site for AMR: 2.0.0.9019@0bcf55d
2023-05-24 16:03:18 +02:00
<li class="nav-item">
Built site for AMR: 1.8.1.9020@d6676e9
2022-08-21 16:59:35 +02:00
<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>Italicise Taxonomic Families, Genera, Species, Subspecies</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/italicise_taxonomy.R" class="external-link"><code>R/italicise_taxonomy.R</code></a></small>
<div class="d-none name"><code>italicise_taxonomy.Rd</code></div>
</div>
<div class="ref-description section level2">
<p>According to the binomial nomenclature, the lowest four taxonomic levels (family, genus, species, subspecies) should be printed in italics. This function finds taxonomic names within strings and makes them italic.</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">italicise_taxonomy</span><span class="op">(</span><span class="va">string</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">"markdown"</span>, <span class="st">"ansi"</span><span class="op">)</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">italicize_taxonomy</span><span class="op">(</span><span class="va">string</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">"markdown"</span>, <span class="st">"ansi"</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>string</dt>
<dd><p>a <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> (vector)</p></dd>
<dt>type</dt>
<dd><p>type of conversion of the taxonomic names, either "markdown" or "ansi", see <em>Details</em></p></dd>
</dl></div>
<div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
<p>This function finds the taxonomic names and makes them italic based on the <a href="microorganisms.html">microorganisms</a> data set.</p>
<p>The taxonomic names can be italicised using markdown (the default) by adding <code>*</code> before and after the taxonomic names, or using ANSI colours by adding <code>\033[3m</code> before and <code>\033[23m</code> after the taxonomic names. If multiple ANSI colours are not available, no conversion will occur.</p>
<p>This function also supports abbreviation of the genus if it is followed by a species, such as "E. coli" and "K. pneumoniae ozaenae".</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="fu">italicise_taxonomy</span><span class="op">(</span><span class="st">"An overview of Staphylococcus aureus isolates"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "An overview of *Staphylococcus aureus* isolates"</span>
<span class="r-in"><span><span class="fu">italicise_taxonomy</span><span class="op">(</span><span class="st">"An overview of S. aureus isolates"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "An overview of *S. aureus* isolates"</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/cat.html" class="external-link">cat</a></span><span class="op">(</span><span class="fu">italicise_taxonomy</span><span class="op">(</span><span class="st">"An overview of S. aureus isolates"</span>, type <span class="op">=</span> <span class="st">"ansi"</span><span class="op">)</span><span class="op">)</span></span></span>
Built site for AMR: 2.0.0.9004@549790c
2023-03-20 22:10:09 +01:00
<span class="r-out co"><span class="r-pr">#&gt;</span> An overview of <span style="font-style: italic;">S. aureus</span> isolates</span>
Built site for AMR: 1.8.1.9020@d6676e9
2022-08-21 16:59:35 +02:00
</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">
Built site for AMR: 1.8.2.9061@eed1c14
2022-12-11 11:50:34 +01:00
<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>
Built site for AMR: 1.8.1.9020@d6676e9
2022-08-21 16:59:35 +02:00
</div>
<div class="pkgdown-footer-right">
Built site for AMR: 1.8.2.9061@eed1c14
2022-12-11 11:50:34 +01:00
<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>
Built site for AMR: 1.8.1.9020@d6676e9
2022-08-21 16:59:35 +02:00
</div>
</footer></div>
</body></html>