AMR/docs/reference/italicise_taxonomy.html

240 lines
14 KiB
HTML
Raw Normal View History

2021-05-03 10:47:32 +02:00
<!DOCTYPE html>
2021-12-12 11:07:02 +01:00
<!-- 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=1.0"><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"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- 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"><!-- 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><!-- 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><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><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 italic. 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="twitter:card" content="summary_large_image"><meta name="twitter:creator" content="@msberends"><meta name="twitter:site" content="@univgroningen"><!-- 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]>
2021-05-03 10:47:32 +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 data-spy="scroll" data-target="#toc">
2021-05-03 10:47:32 +02:00
<div class="container template-reference-topic">
<header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
2021-05-03 10:47:32 +02:00
<div class="container">
<div class="navbar-header">
<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
<span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
2022-03-03 21:11:02 +01:00
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span>
2021-05-03 10:47:32 +02:00
</span>
</div>
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav"><li>
2021-05-03 10:47:32 +02:00
<a href="../index.html">
<span class="fa fa-home"></span>
2021-05-03 10:47:32 +02:00
Home
</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fa fa-question-circle"></span>
2021-05-03 10:47:32 +02:00
How to
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu"><li>
2021-05-03 10:47:32 +02:00
<a href="../articles/AMR.html">
<span class="fa fa-directions"></span>
2021-05-03 10:47:32 +02:00
Conduct AMR analysis
</a>
</li>
<li>
<a href="../articles/resistance_predict.html">
<span class="fa fa-dice"></span>
2021-05-03 10:47:32 +02:00
Predict antimicrobial resistance
</a>
</li>
<li>
<a href="../articles/datasets.html">
<span class="fa fa-database"></span>
2021-05-03 10:47:32 +02:00
Data sets for download / own use
</a>
</li>
<li>
<a href="../articles/PCA.html">
<span class="fa fa-compress"></span>
2021-05-03 10:47:32 +02:00
Conduct principal component analysis for AMR
</a>
</li>
<li>
<a href="../articles/MDR.html">
<span class="fa fa-skull-crossbones"></span>
2021-05-03 10:47:32 +02:00
Determine multi-drug resistance (MDR)
</a>
</li>
<li>
<a href="../articles/WHONET.html">
<span class="fa fa-globe-americas"></span>
2021-05-03 10:47:32 +02:00
Work with WHONET data
</a>
</li>
<li>
<a href="../articles/SPSS.html">
<span class="fa fa-file-upload"></span>
2021-05-03 10:47:32 +02:00
Import data from SPSS/SAS/Stata
</a>
</li>
<li>
<a href="../articles/EUCAST.html">
<span class="fa fa-exchange-alt"></span>
2021-05-03 10:47:32 +02:00
Apply EUCAST rules
</a>
</li>
<li>
<a href="../reference/mo_property.html">
<span class="fa fa-bug"></span>
2021-05-03 10:47:32 +02:00
Get properties of a microorganism
</a>
</li>
<li>
<a href="../reference/ab_property.html">
<span class="fa fa-capsules"></span>
2021-05-03 10:47:32 +02:00
Get properties of an antibiotic
</a>
</li>
<li>
<a href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
2021-05-03 10:47:32 +02:00
Other: benchmarks
</a>
</li>
</ul></li>
2021-05-03 10:47:32 +02:00
<li>
<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
2021-05-03 10:47:32 +02:00
Manual
</a>
</li>
<li>
<a href="../authors.html">
<span class="fa fa-users"></span>
2021-05-03 10:47:32 +02:00
Authors
</a>
</li>
<li>
<a href="../news/index.html">
<span class="far fa-newspaper"></span>
Changelog
</a>
</li>
</ul><ul class="nav navbar-nav navbar-right"><li>
<a href="https://github.com/msberends/AMR" class="external-link">
2021-05-03 10:47:32 +02:00
<span class="fab fa-github"></span>
Source Code
</a>
</li>
</ul></div><!--/.nav-collapse -->
2021-05-03 10:47:32 +02:00
</div><!--/.container -->
</div><!--/.navbar -->
</header><div class="row">
2021-05-03 10:47:32 +02:00
<div class="col-md-9 contents">
<div class="page-header">
<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>
2021-05-03 10:47:32 +02:00
<div class="hidden name"><code>italicise_taxonomy.Rd</code></div>
</div>
<div class="ref-description">
<p>According to the binomial nomenclature, the lowest four taxonomic levels (family, genus, species, subspecies) should be printed in italic. This function finds taxonomic names within strings and makes them italic.</p>
</div>
<div id="ref-usage">
<div class="sourceCode"><pre class="sourceCode r"><code><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 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></code></pre></div>
</div>
<div id="arguments">
<h2>Arguments</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 id="details">
<h2>Details</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>
2021-05-03 10:47:32 +02:00
<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 id="stable-lifecycle">
<h2>Stable Lifecycle</h2>
2021-05-03 10:47:32 +02:00
<p><img src="figures/lifecycle_stable.svg" style='margin-bottom:"5"'><br>
The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
</div>
<div id="read-more-on-our-website-">
<h2>Read more on Our Website!</h2>
2021-05-03 10:47:32 +02:00
<p>On our website <a href="https://msberends.github.io/AMR/">https://msberends.github.io/AMR/</a> you can find <a href="https://msberends.github.io/AMR/articles/AMR.html">a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href="https://msberends.github.io/AMR/reference/">complete documentation of all functions</a> and <a href="https://msberends.github.io/AMR/articles/WHONET.html">an example analysis using WHONET data</a>.</p>
</div>
2021-05-12 18:15:03 +02:00
<div id="ref-examples">
<h2>Examples</h2>
<div class="sourceCode"><pre class="sourceCode r"><code><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 class="fu">italicise_taxonomy</span><span class="op">(</span><span class="st">"An overview of S. aureus isolates"</span><span class="op">)</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 class="co"># since ggplot2 supports no markdown (yet), use</span>
<span class="co"># italicise_taxonomy() and the `ggtext` package for titles:</span>
<span class="co"># \donttest{</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://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span> <span class="op">&amp;&amp;</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://wilkelab.org/ggtext/" class="external-link">"ggtext"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span>
<span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMC</span>,
title <span class="op">=</span> <span class="fu">italicise_taxonomy</span><span class="op">(</span><span class="st">"Amoxi/clav in E. coli"</span><span class="op">)</span><span class="op">)</span> <span class="op">+</span>
<span class="fu"><a href="https://ggplot2.tidyverse.org/reference/theme.html" class="external-link">theme</a></span><span class="op">(</span>plot.title <span class="op">=</span> <span class="fu">ggtext</span><span class="fu">::</span><span class="fu"><a href="https://wilkelab.org/ggtext/reference/element_markdown.html" class="external-link">element_markdown</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span>
<span class="op">}</span>
<span class="co"># }</span>
</code></pre></div>
</div>
2021-05-03 10:47:32 +02:00
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2>
</nav></div>
2021-05-03 10:47:32 +02:00
</div>
<footer><div class="copyright">
2021-12-06 11:12:30 +01:00
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
2021-05-03 10:47:32 +02:00
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
2021-05-03 10:47:32 +02:00
</div>
</footer></div>
2021-05-03 10:47:32 +02:00
2021-05-03 10:47:32 +02:00
</body></html>
2021-05-03 10:47:32 +02:00