P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2024-12-26 18:06:11 +01:00
Code Releases Activity
e2aa4f996b
AMR/docs/articles/benchmarks.html

512 lines
49 KiB
HTML
Raw Blame History

This file contains ambiguous Unicode characters

This file contains Unicode characters that might be confused with other characters. If you think that this is intentional, you can safely ignore this warning. Use the Escape button to reveal them.

<!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=1.0">
<title>Benchmarks • 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/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" crossorigin="anonymous">
<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script><!-- sticky kit --><script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet">
<script src="../pkgdown.js"></script><!-- docsearch --><script src="../docsearch.js"></script><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.css" integrity="sha256-QOSRU/ra9ActyXkIBbiIB144aDBdtvXBcNc3OTNuX/Q=" crossorigin="anonymous">
<link href="../docsearch.css" rel="stylesheet">
<script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/jquery.mark.min.js" integrity="sha256-4HLtjeVgH0eIB3aZ9mLYF6E8oU5chNdjU6p6rrXpl9U=" crossorigin="anonymous"></script><link href="../extra.css" rel="stylesheet">
<script src="../extra.js"></script><meta property="og:title" content="Benchmarks">
<meta property="og:description" content="">
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png">
<meta name="twitter:card" content="summary">
<!-- 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>
<div class="container template-article">
<header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
<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>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9075</span>
</span>
</div>
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
<span class="fa fa-home"></span>
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>
How to
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/AMR.html">
<span class="fa fa-directions"></span>
Conduct AMR analysis
</a>
</li>
<li>
<a href="../articles/resistance_predict.html">
<span class="fa fa-dice"></span>
Predict antimicrobial resistance
</a>
</li>
<li>
<a href="../articles/MDR.html">
<span class="fa fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
</a>
</li>
<li>
<a href="../articles/WHONET.html">
<span class="fa fa-globe-americas"></span>
Work with WHONET data
</a>
</li>
<li>
<a href="../articles/SPSS.html">
<span class="fa fa-file-upload"></span>
Import data from SPSS/SAS/Stata
</a>
</li>
<li>
<a href="../articles/EUCAST.html">
<span class="fa fa-exchange-alt"></span>
Apply EUCAST rules
</a>
</li>
<li>
<a href="../reference/mo_property.html">
<span class="fa fa-bug"></span>
Get properties of a microorganism
</a>
</li>
<li>
<a href="../reference/ab_property.html">
<span class="fa fa-capsules"></span>
Get properties of an antibiotic
</a>
</li>
<li>
<a href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</li>
</ul>
</li>
<li>
<a href="../reference/">
<span class="fa fa-book-open"></span>
Manual
</a>
</li>
<li>
<a href="../authors.html">
<span class="fa fa-users"></span>
Authors
</a>
</li>
<li>
<a href="../news/">
<span class="far fa far fa-newspaper"></span>
Changelog
</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
<span class="fab fa fab fa-gitlab"></span>
Source Code
</a>
</li>
<li>
<a href="../LICENSE-text.html">
<span class="fa fa-book"></span>
Licence
</a>
</li>
</ul>
<form class="navbar-form navbar-right" role="search">
<div class="form-group">
<input type="search" class="form-control" name="search-input" id="search-input" placeholder="Search..." aria-label="Search for..." autocomplete="off">
</div>
</form>
</div>
<!--/.nav-collapse -->
</div>
<!--/.container -->
</div>
<!--/.navbar -->
</header><div class="row">
<div class="col-md-9 contents">
<div class="page-header toc-ignore">
<h1>Benchmarks</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">18 September 2019</h4>
<div class="hidden name"><code>benchmarks.Rmd</code></div>
</div>
<p><small>Source: <a href="https://gitlab.com/msberends/AMR/blob/master/vignettes/benchmarks.Rmd" class="uri">https://gitlab.com/msberends/AMR/blob/master/vignettes/benchmarks.Rmd</a></small></p>
<p>One of the most important features of this package is the complete microbial taxonomic database, supplied by the <a href="http://catalogueoflife.org">Catalogue of Life</a>. We created a function <code><a href="../reference/as.mo.html">as.mo()</a></code> that transforms any user input value to a valid microbial ID by using intelligent rules combined with the taxonomic tree of Catalogue of Life.</p>
<p>Using the <code>microbenchmark</code> package, we can review the calculation performance of this function. Its function <code><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark()</a></code> runs different input expressions independently of each other and measures their time-to-result.</p>
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(microbenchmark)</a>
<a class="sourceLine" id="cb1-2" data-line-number="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(AMR)</a></code></pre></div>
<p>In the next test, we try to ‘coerce’ different input values for <em>Staphylococcus aureus</em>. The actual result is the same every time: it returns its MO code <code>B_STPHY_AURS</code> (<em>B</em> stands for <em>Bacteria</em>, the taxonomic kingdom).</p>
<p>But the calculation time differs a lot:</p>
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" data-line-number="1">S.aureus &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(</a>
<a class="sourceLine" id="cb2-2" data-line-number="2"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"sau"</span>), <span class="co"># WHONET code</span></a>
<a class="sourceLine" id="cb2-3" data-line-number="3"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"stau"</span>),</a>
<a class="sourceLine" id="cb2-4" data-line-number="4"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"STAU"</span>),</a>
<a class="sourceLine" id="cb2-5" data-line-number="5"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"staaur"</span>),</a>
<a class="sourceLine" id="cb2-6" data-line-number="6"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"STAAUR"</span>),</a>
<a class="sourceLine" id="cb2-7" data-line-number="7"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S. aureus"</span>),</a>
<a class="sourceLine" id="cb2-8" data-line-number="8"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S aureus"</span>),</a>
<a class="sourceLine" id="cb2-9" data-line-number="9"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"Staphylococcus aureus"</span>), <span class="co"># official taxonomic name</span></a>
<a class="sourceLine" id="cb2-10" data-line-number="10"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"Staphylococcus aureus (MRSA)"</span>), <span class="co"># additional text</span></a>
<a class="sourceLine" id="cb2-11" data-line-number="11"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"Sthafilokkockus aaureuz"</span>), <span class="co"># incorrect spelling</span></a>
<a class="sourceLine" id="cb2-12" data-line-number="12"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"MRSA"</span>), <span class="co"># Methicillin Resistant S. aureus</span></a>
<a class="sourceLine" id="cb2-13" data-line-number="13"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"VISA"</span>), <span class="co"># Vancomycin Intermediate S. aureus</span></a>
<a class="sourceLine" id="cb2-14" data-line-number="14"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"VRSA"</span>), <span class="co"># Vancomycin Resistant S. aureus</span></a>
<a class="sourceLine" id="cb2-15" data-line-number="15"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="dv">22242419</span>), <span class="co"># Catalogue of Life ID</span></a>
<a class="sourceLine" id="cb2-16" data-line-number="16"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
<a class="sourceLine" id="cb2-17" data-line-number="17"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(S.aureus, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">2</span>)</a>
<a class="sourceLine" id="cb2-18" data-line-number="18"><span class="co"># Unit: milliseconds</span></a>
<a class="sourceLine" id="cb2-19" data-line-number="19"><span class="co"># expr min lq mean median uq</span></a>
<a class="sourceLine" id="cb2-20" data-line-number="20"><span class="co"># as.mo("sau") 8.5 8.9 12.0 9.1 9.7</span></a>
<a class="sourceLine" id="cb2-21" data-line-number="21"><span class="co"># as.mo("stau") 31.0 32.0 48.0 34.0 55.0</span></a>
<a class="sourceLine" id="cb2-22" data-line-number="22"><span class="co"># as.mo("STAU") 31.0 31.0 35.0 32.0 33.0</span></a>
<a class="sourceLine" id="cb2-23" data-line-number="23"><span class="co"># as.mo("staaur") 8.6 8.8 12.0 9.0 9.3</span></a>
<a class="sourceLine" id="cb2-24" data-line-number="24"><span class="co"># as.mo("STAAUR") 8.6 8.9 9.0 9.0 9.1</span></a>
<a class="sourceLine" id="cb2-25" data-line-number="25"><span class="co"># as.mo("S. aureus") 23.0 23.0 26.0 24.0 24.0</span></a>
<a class="sourceLine" id="cb2-26" data-line-number="26"><span class="co"># as.mo("S aureus") 23.0 23.0 31.0 24.0 44.0</span></a>
<a class="sourceLine" id="cb2-27" data-line-number="27"><span class="co"># as.mo("Staphylococcus aureus") 27.0 28.0 29.0 29.0 29.0</span></a>
<a class="sourceLine" id="cb2-28" data-line-number="28"><span class="co"># as.mo("Staphylococcus aureus (MRSA)") 550.0 560.0 590.0 580.0 590.0</span></a>
<a class="sourceLine" id="cb2-29" data-line-number="29"><span class="co"># as.mo("Sthafilokkockus aaureuz") 270.0 290.0 340.0 300.0 330.0</span></a>
<a class="sourceLine" id="cb2-30" data-line-number="30"><span class="co"># as.mo("MRSA") 8.7 8.8 9.1 9.1 9.4</span></a>
<a class="sourceLine" id="cb2-31" data-line-number="31"><span class="co"># as.mo("VISA") 18.0 19.0 20.0 19.0 20.0</span></a>
<a class="sourceLine" id="cb2-32" data-line-number="32"><span class="co"># as.mo("VRSA") 19.0 19.0 23.0 19.0 22.0</span></a>
<a class="sourceLine" id="cb2-33" data-line-number="33"><span class="co"># as.mo(22242419) 18.0 18.0 37.0 30.0 42.0</span></a>
<a class="sourceLine" id="cb2-34" data-line-number="34"><span class="co"># max neval</span></a>
<a class="sourceLine" id="cb2-35" data-line-number="35"><span class="co"># 31.0 10</span></a>
<a class="sourceLine" id="cb2-36" data-line-number="36"><span class="co"># 120.0 10</span></a>
<a class="sourceLine" id="cb2-37" data-line-number="37"><span class="co"># 59.0 10</span></a>
<a class="sourceLine" id="cb2-38" data-line-number="38"><span class="co"># 34.0 10</span></a>
<a class="sourceLine" id="cb2-39" data-line-number="39"><span class="co"># 9.2 10</span></a>
<a class="sourceLine" id="cb2-40" data-line-number="40"><span class="co"># 49.0 10</span></a>
<a class="sourceLine" id="cb2-41" data-line-number="41"><span class="co"># 53.0 10</span></a>
<a class="sourceLine" id="cb2-42" data-line-number="42"><span class="co"># 30.0 10</span></a>
<a class="sourceLine" id="cb2-43" data-line-number="43"><span class="co"># 670.0 10</span></a>
<a class="sourceLine" id="cb2-44" data-line-number="44"><span class="co"># 620.0 10</span></a>
<a class="sourceLine" id="cb2-45" data-line-number="45"><span class="co"># 9.5 10</span></a>
<a class="sourceLine" id="cb2-46" data-line-number="46"><span class="co"># 28.0 10</span></a>
<a class="sourceLine" id="cb2-47" data-line-number="47"><span class="co"># 45.0 10</span></a>
<a class="sourceLine" id="cb2-48" data-line-number="48"><span class="co"># 110.0 10</span></a></code></pre></div>
<p><img src="benchmarks_files/figure-html/unnamed-chunk-4-1.png" width="562.5"></p>
<p>In the table above, all measurements are shown in milliseconds (thousands of seconds). A value of 5 milliseconds means it can determine 200 input values per second. It case of 100 milliseconds, this is only 10 input values per second. The second input is the only one that has to be looked up thoroughly. All the others are known codes (the first one is a WHONET code) or common laboratory codes, or common full organism names like the last one. Full organism names are always preferred.</p>
<p>To achieve this speed, the <code>as.mo</code> function also takes into account the prevalence of human pathogenic microorganisms. The downside is of course that less prevalent microorganisms will be determined less fast. See this example for the ID of <em>Thermus islandicus</em> (<code>B_THERMS_ISLN</code>), a bug probably never found before in humans:</p>
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" data-line-number="1">T.islandicus &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"theisl"</span>),</a>
<a class="sourceLine" id="cb3-2" data-line-number="2"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"THEISL"</span>),</a>
<a class="sourceLine" id="cb3-3" data-line-number="3"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"T. islandicus"</span>),</a>
<a class="sourceLine" id="cb3-4" data-line-number="4"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"T. islandicus"</span>),</a>
<a class="sourceLine" id="cb3-5" data-line-number="5"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"Thermus islandicus"</span>),</a>
<a class="sourceLine" id="cb3-6" data-line-number="6"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
<a class="sourceLine" id="cb3-7" data-line-number="7"><span class="co"># Warning: </span></a>
<a class="sourceLine" id="cb3-8" data-line-number="8"><span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span></a>
<a class="sourceLine" id="cb3-9" data-line-number="9"></a>
<a class="sourceLine" id="cb3-10" data-line-number="10"><span class="co"># Warning: </span></a>
<a class="sourceLine" id="cb3-11" data-line-number="11"><span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span></a>
<a class="sourceLine" id="cb3-12" data-line-number="12"></a>
<a class="sourceLine" id="cb3-13" data-line-number="13"><span class="co"># Warning: </span></a>
<a class="sourceLine" id="cb3-14" data-line-number="14"><span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span></a>
<a class="sourceLine" id="cb3-15" data-line-number="15"></a>
<a class="sourceLine" id="cb3-16" data-line-number="16"><span class="co"># Warning: </span></a>
<a class="sourceLine" id="cb3-17" data-line-number="17"><span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span></a>
<a class="sourceLine" id="cb3-18" data-line-number="18"></a>
<a class="sourceLine" id="cb3-19" data-line-number="19"><span class="co"># Warning: </span></a>
<a class="sourceLine" id="cb3-20" data-line-number="20"><span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span></a>
<a class="sourceLine" id="cb3-21" data-line-number="21"></a>
<a class="sourceLine" id="cb3-22" data-line-number="22"><span class="co"># Warning: </span></a>
<a class="sourceLine" id="cb3-23" data-line-number="23"><span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span></a>
<a class="sourceLine" id="cb3-24" data-line-number="24"></a>
<a class="sourceLine" id="cb3-25" data-line-number="25"><span class="co"># Warning: </span></a>
<a class="sourceLine" id="cb3-26" data-line-number="26"><span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span></a>
<a class="sourceLine" id="cb3-27" data-line-number="27"></a>
<a class="sourceLine" id="cb3-28" data-line-number="28"><span class="co"># Warning: </span></a>
<a class="sourceLine" id="cb3-29" data-line-number="29"><span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span></a>
<a class="sourceLine" id="cb3-30" data-line-number="30"></a>
<a class="sourceLine" id="cb3-31" data-line-number="31"><span class="co"># Warning: </span></a>
<a class="sourceLine" id="cb3-32" data-line-number="32"><span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span></a>
<a class="sourceLine" id="cb3-33" data-line-number="33"></a>
<a class="sourceLine" id="cb3-34" data-line-number="34"><span class="co"># Warning: </span></a>
<a class="sourceLine" id="cb3-35" data-line-number="35"><span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span></a>
<a class="sourceLine" id="cb3-36" data-line-number="36"></a>
<a class="sourceLine" id="cb3-37" data-line-number="37"><span class="co"># Warning: </span></a>
<a class="sourceLine" id="cb3-38" data-line-number="38"><span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span></a>
<a class="sourceLine" id="cb3-39" data-line-number="39"></a>
<a class="sourceLine" id="cb3-40" data-line-number="40"><span class="co"># Warning: </span></a>
<a class="sourceLine" id="cb3-41" data-line-number="41"><span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span></a>
<a class="sourceLine" id="cb3-42" data-line-number="42"></a>
<a class="sourceLine" id="cb3-43" data-line-number="43"><span class="co"># Warning: </span></a>
<a class="sourceLine" id="cb3-44" data-line-number="44"><span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span></a>
<a class="sourceLine" id="cb3-45" data-line-number="45"></a>
<a class="sourceLine" id="cb3-46" data-line-number="46"><span class="co"># Warning: </span></a>
<a class="sourceLine" id="cb3-47" data-line-number="47"><span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span></a>
<a class="sourceLine" id="cb3-48" data-line-number="48"></a>
<a class="sourceLine" id="cb3-49" data-line-number="49"><span class="co"># Warning: </span></a>
<a class="sourceLine" id="cb3-50" data-line-number="50"><span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span></a>
<a class="sourceLine" id="cb3-51" data-line-number="51"></a>
<a class="sourceLine" id="cb3-52" data-line-number="52"><span class="co"># Warning: </span></a>
<a class="sourceLine" id="cb3-53" data-line-number="53"><span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span></a>
<a class="sourceLine" id="cb3-54" data-line-number="54"></a>
<a class="sourceLine" id="cb3-55" data-line-number="55"><span class="co"># Warning: </span></a>
<a class="sourceLine" id="cb3-56" data-line-number="56"><span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span></a>
<a class="sourceLine" id="cb3-57" data-line-number="57"></a>
<a class="sourceLine" id="cb3-58" data-line-number="58"><span class="co"># Warning: </span></a>
<a class="sourceLine" id="cb3-59" data-line-number="59"><span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span></a>
<a class="sourceLine" id="cb3-60" data-line-number="60"></a>
<a class="sourceLine" id="cb3-61" data-line-number="61"><span class="co"># Warning: </span></a>
<a class="sourceLine" id="cb3-62" data-line-number="62"><span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span></a>
<a class="sourceLine" id="cb3-63" data-line-number="63"></a>
<a class="sourceLine" id="cb3-64" data-line-number="64"><span class="co"># Warning: </span></a>
<a class="sourceLine" id="cb3-65" data-line-number="65"><span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span></a>
<a class="sourceLine" id="cb3-66" data-line-number="66"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(T.islandicus, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">2</span>)</a>
<a class="sourceLine" id="cb3-67" data-line-number="67"><span class="co"># Unit: milliseconds</span></a>
<a class="sourceLine" id="cb3-68" data-line-number="68"><span class="co"># expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb3-69" data-line-number="69"><span class="co"># as.mo("theisl") 1300 1400 1400 1400 1500 1600 10</span></a>
<a class="sourceLine" id="cb3-70" data-line-number="70"><span class="co"># as.mo("THEISL") 1400 1400 1400 1400 1500 1600 10</span></a>
<a class="sourceLine" id="cb3-71" data-line-number="71"><span class="co"># as.mo("T. islandicus") 370 400 410 410 420 450 10</span></a>
<a class="sourceLine" id="cb3-72" data-line-number="72"><span class="co"># as.mo("T. islandicus") 360 370 400 380 410 490 10</span></a>
<a class="sourceLine" id="cb3-73" data-line-number="73"><span class="co"># as.mo("Thermus islandicus") 28 30 35 32 35 59 10</span></a></code></pre></div>
<p>That takes 8.5 times as much time on average. A value of 100 milliseconds means it can only determine ~10 different input values per second. We can conclude that looking up arbitrary codes of less prevalent microorganisms is the worst way to go, in terms of calculation performance. Full names (like <em>Thermus islandicus</em>) are almost fast - these are the most probable input from most data sets.</p>
<p>In the figure below, we compare <em>Escherichia coli</em> (which is very common) with <em>Prevotella brevis</em> (which is moderately common) and with <em>Thermus islandicus</em> (which is uncommon):</p>
<pre><code># Warning:
# Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.
# NOTE: Prevotella ruminicola brevis (Shah et al., 1990) was renamed Prevotella brevis (Avgustin et al., 2016) [B_PRVTL_BRVS]
# Warning:
# Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.
# NOTE: Prevotella ruminicola brevis (Shah et al., 1990) was renamed Prevotella brevis (Avgustin et al., 2016) [B_PRVTL_BRVS]
# NOTE: Prevotella ruminicola brevis (Shah et al., 1990) was renamed Prevotella brevis (Avgustin et al., 2016) [B_PRVTL_BRVS]
# Warning:
# Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.
# Warning:
# Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.
# NOTE: Prevotella ruminicola brevis (Shah et al., 1990) was renamed Prevotella brevis (Avgustin et al., 2016) [B_PRVTL_BRVS]
# NOTE: Prevotella ruminicola brevis (Shah et al., 1990) was renamed Prevotella brevis (Avgustin et al., 2016) [B_PRVTL_BRVS]
# Warning:
# Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.
# NOTE: Prevotella ruminicola brevis (Shah et al., 1990) was renamed Prevotella brevis (Avgustin et al., 2016) [B_PRVTL_BRVS]
# NOTE: Prevotella ruminicola brevis (Shah et al., 1990) was renamed Prevotella brevis (Avgustin et al., 2016) [B_PRVTL_BRVS]
# Warning:
# Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.
# Warning:
# Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.
# Warning:
# Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.
# Warning:
# Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.
# NOTE: Prevotella ruminicola brevis (Shah et al., 1990) was renamed Prevotella brevis (Avgustin et al., 2016) [B_PRVTL_BRVS]
# NOTE: Prevotella ruminicola brevis (Shah et al., 1990) was renamed Prevotella brevis (Avgustin et al., 2016) [B_PRVTL_BRVS]
# NOTE: Prevotella ruminicola brevis (Shah et al., 1990) was renamed Prevotella brevis (Avgustin et al., 2016) [B_PRVTL_BRVS]
# Warning:
# Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</code></pre>
<p><img src="benchmarks_files/figure-html/unnamed-chunk-6-1.png" width="562.5"></p>
<p>In reality, the <code><a href="../reference/as.mo.html">as.mo()</a></code> functions <strong>learns from its own output to speed up determinations for next times</strong>. In above figure, this effect was disabled to show the difference with the boxplot below - when you would use <code><a href="../reference/as.mo.html">as.mo()</a></code> yourself:</p>
<pre><code># NOTE: results are saved to /Users/msberends/Library/R/3.6/library/AMR/mo_history/mo_history.csv.
# NOTE: Prevotella ruminicola brevis (Shah et al., 1990) was renamed Prevotella brevis (Avgustin et al., 2016) [B_PRVTL_BRVS]
# Warning:
# Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</code></pre>
<p><img src="benchmarks_files/figure-html/unnamed-chunk-7-1.png" width="562.5"></p>
<p>The highest outliers are the first times. All next determinations were done in only thousands of seconds.</p>
<p>Uncommon microorganisms take a lot more time than common microorganisms. To relieve this pitfall and further improve performance, two important calculations take almost no time at all: <strong>repetitive results</strong> and <strong>already precalculated results</strong>.</p>
<div id="repetitive-results" class="section level3">
<h3 class="hasAnchor">
<a href="#repetitive-results" class="anchor"></a>Repetitive results</h3>
<p>Repetitive results are unique values that are present more than once. Unique values will only be calculated once by <code><a href="../reference/as.mo.html">as.mo()</a></code>. We will use <code><a href="../reference/mo_property.html">mo_name()</a></code> for this test - a helper function that returns the full microbial name (genus, species and possibly subspecies) which uses <code><a href="../reference/as.mo.html">as.mo()</a></code> internally.</p>
<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(dplyr)</a>
<a class="sourceLine" id="cb6-2" data-line-number="2"><span class="co"># take all MO codes from the example_isolates data set</span></a>
<a class="sourceLine" id="cb6-3" data-line-number="3">x &lt;-<span class="st"> </span>example_isolates<span class="op">$</span>mo <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb6-4" data-line-number="4"><span class="st"> </span><span class="co"># keep only the unique ones</span></a>
<a class="sourceLine" id="cb6-5" data-line-number="5"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/unique">unique</a></span>() <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb6-6" data-line-number="6"><span class="st"> </span><span class="co"># pick 50 of them at random</span></a>
<a class="sourceLine" id="cb6-7" data-line-number="7"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/sample.html">sample</a></span>(<span class="dv">50</span>) <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb6-8" data-line-number="8"><span class="st"> </span><span class="co"># paste that 10,000 times</span></a>
<a class="sourceLine" id="cb6-9" data-line-number="9"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/rep">rep</a></span>(<span class="dv">10000</span>) <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb6-10" data-line-number="10"><span class="st"> </span><span class="co"># scramble it</span></a>
<a class="sourceLine" id="cb6-11" data-line-number="11"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/sample.html">sample</a></span>()</a>
<a class="sourceLine" id="cb6-12" data-line-number="12"> </a>
<a class="sourceLine" id="cb6-13" data-line-number="13"><span class="co"># got indeed 50 times 10,000 = half a million?</span></a>
<a class="sourceLine" id="cb6-14" data-line-number="14"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/length">length</a></span>(x)</a>
<a class="sourceLine" id="cb6-15" data-line-number="15"><span class="co"># [1] 500000</span></a>
<a class="sourceLine" id="cb6-16" data-line-number="16"></a>
<a class="sourceLine" id="cb6-17" data-line-number="17"><span class="co"># and how many unique values do we have?</span></a>
<a class="sourceLine" id="cb6-18" data-line-number="18"><span class="kw"><a href="https://dplyr.tidyverse.org/reference/n_distinct.html">n_distinct</a></span>(x)</a>
<a class="sourceLine" id="cb6-19" data-line-number="19"><span class="co"># [1] 50</span></a>
<a class="sourceLine" id="cb6-20" data-line-number="20"></a>
<a class="sourceLine" id="cb6-21" data-line-number="21"><span class="co"># now let's see:</span></a>
<a class="sourceLine" id="cb6-22" data-line-number="22">run_it &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(x),</a>
<a class="sourceLine" id="cb6-23" data-line-number="23"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
<a class="sourceLine" id="cb6-24" data-line-number="24"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">3</span>)</a>
<a class="sourceLine" id="cb6-25" data-line-number="25"><span class="co"># Unit: milliseconds</span></a>
<a class="sourceLine" id="cb6-26" data-line-number="26"><span class="co"># expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb6-27" data-line-number="27"><span class="co"># mo_name(x) 610 644 669 665 684 748 10</span></a></code></pre></div>
<p>So transforming 500,000 values (!!) of 50 unique values only takes 0.66 seconds (664 ms). You only lose time on your unique input values.</p>
</div>
<div id="precalculated-results" class="section level3">
<h3 class="hasAnchor">
<a href="#precalculated-results" class="anchor"></a>Precalculated results</h3>
<p>What about precalculated results? If the input is an already precalculated result of a helper function like <code><a href="../reference/mo_property.html">mo_name()</a></code>, it almost doesn’t take any time at all (see ‘C’ below):</p>
<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" data-line-number="1">run_it &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="dt">A =</span> <span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"B_STPHY_AURS"</span>),</a>
<a class="sourceLine" id="cb7-2" data-line-number="2"> <span class="dt">B =</span> <span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"S. aureus"</span>),</a>
<a class="sourceLine" id="cb7-3" data-line-number="3"> <span class="dt">C =</span> <span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"Staphylococcus aureus"</span>),</a>
<a class="sourceLine" id="cb7-4" data-line-number="4"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
<a class="sourceLine" id="cb7-5" data-line-number="5"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">3</span>)</a>
<a class="sourceLine" id="cb7-6" data-line-number="6"><span class="co"># Unit: milliseconds</span></a>
<a class="sourceLine" id="cb7-7" data-line-number="7"><span class="co"># expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb7-8" data-line-number="8"><span class="co"># A 6.150 6.260 6.400 6.390 6.520 6.710 10</span></a>
<a class="sourceLine" id="cb7-9" data-line-number="9"><span class="co"># B 22.200 22.500 26.400 22.700 24.800 53.100 10</span></a>
<a class="sourceLine" id="cb7-10" data-line-number="10"><span class="co"># C 0.645 0.774 0.801 0.803 0.812 0.911 10</span></a></code></pre></div>
<p>So going from <code><a href="../reference/mo_property.html">mo_name("Staphylococcus aureus")</a></code> to <code>"Staphylococcus aureus"</code> takes 0.0008 seconds - it doesn’t even start calculating <em>if the result would be the same as the expected resulting value</em>. That goes for all helper functions:</p>
<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" data-line-number="1">run_it &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="dt">A =</span> <span class="kw"><a href="../reference/mo_property.html">mo_species</a></span>(<span class="st">"aureus"</span>),</a>
<a class="sourceLine" id="cb8-2" data-line-number="2"> <span class="dt">B =</span> <span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="st">"Staphylococcus"</span>),</a>
<a class="sourceLine" id="cb8-3" data-line-number="3"> <span class="dt">C =</span> <span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"Staphylococcus aureus"</span>),</a>
<a class="sourceLine" id="cb8-4" data-line-number="4"> <span class="dt">D =</span> <span class="kw"><a href="../reference/mo_property.html">mo_family</a></span>(<span class="st">"Staphylococcaceae"</span>),</a>
<a class="sourceLine" id="cb8-5" data-line-number="5"> <span class="dt">E =</span> <span class="kw"><a href="../reference/mo_property.html">mo_order</a></span>(<span class="st">"Bacillales"</span>),</a>
<a class="sourceLine" id="cb8-6" data-line-number="6"> <span class="dt">F =</span> <span class="kw"><a href="../reference/mo_property.html">mo_class</a></span>(<span class="st">"Bacilli"</span>),</a>
<a class="sourceLine" id="cb8-7" data-line-number="7"> <span class="dt">G =</span> <span class="kw"><a href="../reference/mo_property.html">mo_phylum</a></span>(<span class="st">"Firmicutes"</span>),</a>
<a class="sourceLine" id="cb8-8" data-line-number="8"> <span class="dt">H =</span> <span class="kw"><a href="../reference/mo_property.html">mo_kingdom</a></span>(<span class="st">"Bacteria"</span>),</a>
<a class="sourceLine" id="cb8-9" data-line-number="9"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
<a class="sourceLine" id="cb8-10" data-line-number="10"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">3</span>)</a>
<a class="sourceLine" id="cb8-11" data-line-number="11"><span class="co"># Unit: milliseconds</span></a>
<a class="sourceLine" id="cb8-12" data-line-number="12"><span class="co"># expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb8-13" data-line-number="13"><span class="co"># A 0.467 0.471 0.509 0.492 0.512 0.680 10</span></a>
<a class="sourceLine" id="cb8-14" data-line-number="14"><span class="co"># B 0.628 0.634 0.664 0.646 0.685 0.748 10</span></a>
<a class="sourceLine" id="cb8-15" data-line-number="15"><span class="co"># C 0.712 0.723 0.771 0.755 0.797 0.906 10</span></a>
<a class="sourceLine" id="cb8-16" data-line-number="16"><span class="co"># D 0.444 0.455 0.475 0.464 0.501 0.518 10</span></a>
<a class="sourceLine" id="cb8-17" data-line-number="17"><span class="co"># E 0.452 0.453 0.468 0.457 0.487 0.510 10</span></a>
<a class="sourceLine" id="cb8-18" data-line-number="18"><span class="co"># F 0.439 0.450 0.462 0.459 0.470 0.501 10</span></a>
<a class="sourceLine" id="cb8-19" data-line-number="19"><span class="co"># G 0.450 0.460 0.476 0.480 0.492 0.496 10</span></a>
<a class="sourceLine" id="cb8-20" data-line-number="20"><span class="co"># H 0.443 0.455 0.461 0.456 0.466 0.495 10</span></a></code></pre></div>
<p>Of course, when running <code><a href="../reference/mo_property.html">mo_phylum("Firmicutes")</a></code> the function has zero knowledge about the actual microorganism, namely <em>S. aureus</em>. But since the result would be <code>"Firmicutes"</code> too, there is no point in calculating the result. And because this package ‘knows’ all phyla of all known bacteria (according to the Catalogue of Life), it can just return the initial value immediately.</p>
</div>
<div id="results-in-other-languages" class="section level3">
<h3 class="hasAnchor">
<a href="#results-in-other-languages" class="anchor"></a>Results in other languages</h3>
<p>When the system language is non-English and supported by this <code>AMR</code> package, some functions will have a translated result. This almost does’t take extra time:</p>
<div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb9-1" data-line-number="1"><span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"en"</span>) <span class="co"># or just mo_name("CoNS") on an English system</span></a>
<a class="sourceLine" id="cb9-2" data-line-number="2"><span class="co"># [1] "Coagulase-negative Staphylococcus (CoNS)"</span></a>
<a class="sourceLine" id="cb9-3" data-line-number="3"></a>
<a class="sourceLine" id="cb9-4" data-line-number="4"><span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"es"</span>) <span class="co"># or just mo_name("CoNS") on a Spanish system</span></a>
<a class="sourceLine" id="cb9-5" data-line-number="5"><span class="co"># [1] "Staphylococcus coagulasa negativo (SCN)"</span></a>
<a class="sourceLine" id="cb9-6" data-line-number="6"></a>
<a class="sourceLine" id="cb9-7" data-line-number="7"><span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"nl"</span>) <span class="co"># or just mo_name("CoNS") on a Dutch system</span></a>
<a class="sourceLine" id="cb9-8" data-line-number="8"><span class="co"># [1] "Coagulase-negatieve Staphylococcus (CNS)"</span></a>
<a class="sourceLine" id="cb9-9" data-line-number="9"></a>
<a class="sourceLine" id="cb9-10" data-line-number="10">run_it &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="dt">en =</span> <span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"en"</span>),</a>
<a class="sourceLine" id="cb9-11" data-line-number="11"> <span class="dt">de =</span> <span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"de"</span>),</a>
<a class="sourceLine" id="cb9-12" data-line-number="12"> <span class="dt">nl =</span> <span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"nl"</span>),</a>
<a class="sourceLine" id="cb9-13" data-line-number="13"> <span class="dt">es =</span> <span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"es"</span>),</a>
<a class="sourceLine" id="cb9-14" data-line-number="14"> <span class="dt">it =</span> <span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"it"</span>),</a>
<a class="sourceLine" id="cb9-15" data-line-number="15"> <span class="dt">fr =</span> <span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"fr"</span>),</a>
<a class="sourceLine" id="cb9-16" data-line-number="16"> <span class="dt">pt =</span> <span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"pt"</span>),</a>
<a class="sourceLine" id="cb9-17" data-line-number="17"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
<a class="sourceLine" id="cb9-18" data-line-number="18"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">4</span>)</a>
<a class="sourceLine" id="cb9-19" data-line-number="19"><span class="co"># Unit: milliseconds</span></a>
<a class="sourceLine" id="cb9-20" data-line-number="20"><span class="co"># expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb9-21" data-line-number="21"><span class="co"># en 18.19 18.35 18.84 18.65 18.99 20.91 10</span></a>
<a class="sourceLine" id="cb9-22" data-line-number="22"><span class="co"># de 19.31 19.71 20.39 20.29 20.92 21.83 10</span></a>
<a class="sourceLine" id="cb9-23" data-line-number="23"><span class="co"># nl 24.43 24.92 25.51 25.37 25.65 27.97 10</span></a>
<a class="sourceLine" id="cb9-24" data-line-number="24"><span class="co"># es 19.22 19.53 20.06 19.82 20.47 21.81 10</span></a>
<a class="sourceLine" id="cb9-25" data-line-number="25"><span class="co"># it 19.36 20.03 24.77 20.26 20.96 45.31 10</span></a>
<a class="sourceLine" id="cb9-26" data-line-number="26"><span class="co"># fr 19.11 19.30 19.71 19.72 20.11 20.37 10</span></a>
<a class="sourceLine" id="cb9-27" data-line-number="27"><span class="co"># pt 19.40 19.90 27.80 21.38 41.88 45.37 10</span></a></code></pre></div>
<p>Currently supported are German, Dutch, Spanish, Italian, French and Portuguese.</p>
</div>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
</div>
</div>
<footer><div class="copyright">
<p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/">Alex W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/">Corinna Glasner</a>.</p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
</footer>
</div>
<script src="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.js" integrity="sha256-GKvGqXDznoRYHCwKXGnuchvKSwmx9SRMrZOTh2g4Sb0=" crossorigin="anonymous"></script><script>
docsearch({
apiKey: 'f737050abfd4d726c63938e18f8c496e',
indexName: 'amr',
inputSelector: 'input#search-input.form-control',
transformData: function(hits) {
return hits.map(function (hit) {
hit.url = updateHitURL(hit);
return hit;
});
}
});
</script>
</body>
</html>
View Git Blame Copy Permalink