mirror of
https://github.com/msberends/AMR.git
synced 2024-12-26 18:46:13 +01:00
397 lines
37 KiB
HTML
397 lines
37 KiB
HTML
<!DOCTYPE html>
|
||
<!-- Generated by pkgdown: do not edit by hand --><html lang="en">
|
||
<head>
|
||
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
|
||
<meta charset="utf-8">
|
||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||
<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="Released version">0.5.0.9017</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/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/atc_property.html">
|
||
<span class="fa fa-capsules"></span>
|
||
|
||
Get properties of an antibiotic
|
||
</a>
|
||
</li>
|
||
<li>
|
||
<a href="../articles/freq.html">
|
||
<span class="fa fa-sort-amount-down"></span>
|
||
|
||
Create frequency tables
|
||
</a>
|
||
</li>
|
||
<li>
|
||
<a href="../articles/G_test.html">
|
||
<span class="fa fa-clipboard-check"></span>
|
||
|
||
Use the G-test
|
||
</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">14 February 2019</h4>
|
||
|
||
|
||
<div class="hidden name"><code>benchmarks.Rmd</code></div>
|
||
|
||
</div>
|
||
|
||
|
||
|
||
<p>One of the most important features of this package is the complete microbial taxonomic database, supplied by ITIS (<a href="https://www.itis.gov" class="uri">https://www.itis.gov</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 AI (Artificial Intelligence) and based on the taxonomic tree of ITIS.</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> calculates different input expressions independently of each others and runs every expression 100 times.</p>
|
||
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" title="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" title="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_AUR</code> (<em>B</em> stands for <em>Bacteria</em>, the taxonomic kingdom).</p>
|
||
<p>But the calculation time differs a lot. Here, the AI effect can be reviewed best:</p>
|
||
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" title="1">benchmark <-<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">"sau"</span>),</a>
|
||
<a class="sourceLine" id="cb2-2" title="2"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"stau"</span>),</a>
|
||
<a class="sourceLine" id="cb2-3" title="3"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"staaur"</span>),</a>
|
||
<a class="sourceLine" id="cb2-4" title="4"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S. aureus"</span>),</a>
|
||
<a class="sourceLine" id="cb2-5" title="5"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S. aureus"</span>),</a>
|
||
<a class="sourceLine" id="cb2-6" title="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" title="7"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"Staphylococcus aureus"</span>),</a>
|
||
<a class="sourceLine" id="cb2-8" title="8"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"B_STPHY_AUR"</span>))</a>
|
||
<a class="sourceLine" id="cb2-9" title="9"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(benchmark, <span class="dt">unit =</span> <span class="st">"ms"</span>)</a>
|
||
<a class="sourceLine" id="cb2-10" title="10"><span class="co"># Unit: milliseconds</span></a>
|
||
<a class="sourceLine" id="cb2-11" title="11"><span class="co"># expr min lq mean median uq max neval</span></a>
|
||
<a class="sourceLine" id="cb2-12" title="12"><span class="co"># as.mo("sau") 18.983141 19.121148 19.9676944 19.1967505 19.2871260 38.635012 100</span></a>
|
||
<a class="sourceLine" id="cb2-13" title="13"><span class="co"># as.mo("stau") 37.503863 37.692049 38.9856547 37.8244335 37.9851040 57.576107 100</span></a>
|
||
<a class="sourceLine" id="cb2-14" title="14"><span class="co"># as.mo("staaur") 18.945427 19.122579 19.6392560 19.2241285 19.3536140 38.687672 100</span></a>
|
||
<a class="sourceLine" id="cb2-15" title="15"><span class="co"># as.mo("S. aureus") 15.305229 15.471103 16.3477096 15.5545630 15.6689280 36.363005 100</span></a>
|
||
<a class="sourceLine" id="cb2-16" title="16"><span class="co"># as.mo("S. aureus") 15.308232 15.469881 16.5269706 15.5506870 15.6277560 42.155292 100</span></a>
|
||
<a class="sourceLine" id="cb2-17" title="17"><span class="co"># as.mo("STAAUR") 18.984049 19.117166 19.6104597 19.2219285 19.3161095 38.638783 100</span></a>
|
||
<a class="sourceLine" id="cb2-18" title="18"><span class="co"># as.mo("Staphylococcus aureus") 8.103546 8.198285 8.6422018 8.2636915 8.3200535 27.002527 100</span></a>
|
||
<a class="sourceLine" id="cb2-19" title="19"><span class="co"># as.mo("B_STPHY_AUR") 0.156236 0.196779 0.2017926 0.2035535 0.2115505 0.241861 100</span></a>
|
||
<a class="sourceLine" id="cb2-20" title="20"></a>
|
||
<a class="sourceLine" id="cb2-21" title="21"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/par">par</a></span>(<span class="dt">mar =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dv">5</span>, <span class="dv">15</span>, <span class="dv">4</span>, <span class="dv">2</span>)) <span class="co"># set more space for left margin text (15)</span></a>
|
||
<a class="sourceLine" id="cb2-22" title="22"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/boxplot">boxplot</a></span>(benchmark, <span class="dt">horizontal =</span> <span class="ot">TRUE</span>, <span class="dt">las =</span> <span class="dv">1</span>, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">log =</span> <span class="ot">FALSE</span>, <span class="dt">xlab =</span> <span class="st">""</span>, <span class="dt">ylim =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dv">0</span>, <span class="dv">200</span>),</a>
|
||
<a class="sourceLine" id="cb2-23" title="23"> <span class="dt">main =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/expression">expression</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/paste">paste</a></span>(<span class="st">"Benchmark of "</span>, <span class="kw"><a href="https://www.rdocumentation.org/packages/grDevices/topics/plotmath">italic</a></span>(<span class="st">"Staphylococcus aureus"</span>))))</a></code></pre></div>
|
||
<p><img src="../reference/figures/benchmark_1.png"></p>
|
||
<p>In the table above, all measurements are shown in milliseconds (thousands of seconds), tested on a quite regular Linux server from 2007 (Core 2 Duo 2.7 GHz, 2 GB DDR2 RAM). A value of 8 milliseconds means it can determine 125 input values per second. It case of 40 milliseconds, this is only 25 input values per second. The more an input value resembles a full name, the faster the result will be found. In case of <code><a href="../reference/as.mo.html">as.mo("B_STPHY_AUR")</a></code>, the input is already a valid MO code, so it only almost takes no time at all (0.0002 seconds on our server).</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 far less faster. See this example for the ID of <em>Burkholderia nodosa</em> (<code>B_BRKHL_NOD</code>):</p>
|
||
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" title="1">benchmark <-<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">"buno"</span>),</a>
|
||
<a class="sourceLine" id="cb3-2" title="2"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"burnod"</span>),</a>
|
||
<a class="sourceLine" id="cb3-3" title="3"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"B. nodosa"</span>),</a>
|
||
<a class="sourceLine" id="cb3-4" title="4"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"B. nodosa"</span>),</a>
|
||
<a class="sourceLine" id="cb3-5" title="5"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"BURNOD"</span>),</a>
|
||
<a class="sourceLine" id="cb3-6" title="6"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"Burkholderia nodosa"</span>),</a>
|
||
<a class="sourceLine" id="cb3-7" title="7"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"B_BRKHL_NOD"</span>))</a>
|
||
<a class="sourceLine" id="cb3-8" title="8"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(benchmark, <span class="dt">unit =</span> <span class="st">"ms"</span>)</a>
|
||
<a class="sourceLine" id="cb3-9" title="9"></a>
|
||
<a class="sourceLine" id="cb3-10" title="10"><span class="co"># Unit: milliseconds</span></a>
|
||
<a class="sourceLine" id="cb3-11" title="11"><span class="co"># expr min lq mean median uq max neval</span></a>
|
||
<a class="sourceLine" id="cb3-12" title="12"><span class="co"># as.mo("buno") 125.141333 125.8553210 129.5727691 126.3899910 127.0954925 194.51985 100</span></a>
|
||
<a class="sourceLine" id="cb3-13" title="13"><span class="co"># as.mo("burnod") 142.300359 144.1611750 147.0642288 144.6074960 145.5243025 176.91649 100</span></a>
|
||
<a class="sourceLine" id="cb3-14" title="14"><span class="co"># as.mo("B. nodosa") 81.530132 81.9360840 83.3915418 82.1852770 82.6848870 102.63184 100</span></a>
|
||
<a class="sourceLine" id="cb3-15" title="15"><span class="co"># as.mo("B. nodosa") 81.109547 81.9836805 84.7595894 82.3437825 82.8282705 110.67036 100</span></a>
|
||
<a class="sourceLine" id="cb3-16" title="16"><span class="co"># as.mo("BURNOD") 143.163527 143.9134485 148.7192688 144.5582580 145.7489115 314.92070 100</span></a>
|
||
<a class="sourceLine" id="cb3-17" title="17"><span class="co"># as.mo("Burkholderia nodosa") 36.226325 36.5499000 37.1309929 36.6581540 36.7551985 56.25597 100</span></a>
|
||
<a class="sourceLine" id="cb3-18" title="18"><span class="co"># as.mo("B_BRKHL_NOD") 0.172509 0.3038455 0.4806591 0.3078265 0.3121215 19.16173 100</span></a>
|
||
<a class="sourceLine" id="cb3-19" title="19"></a>
|
||
<a class="sourceLine" id="cb3-20" title="20"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/boxplot">boxplot</a></span>(benchmark, <span class="dt">horizontal =</span> <span class="ot">TRUE</span>, <span class="dt">las =</span> <span class="dv">1</span>, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">log =</span> <span class="ot">FALSE</span>, <span class="dt">xlab =</span> <span class="st">""</span>, <span class="dt">ylim =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dv">0</span>, <span class="dv">200</span>),</a>
|
||
<a class="sourceLine" id="cb3-21" title="21"> <span class="dt">main =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/expression">expression</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/paste">paste</a></span>(<span class="st">"Benchmark of "</span>, <span class="kw"><a href="https://www.rdocumentation.org/packages/grDevices/topics/plotmath">italic</a></span>(<span class="st">"Burkholderia nodosa"</span>))))</a></code></pre></div>
|
||
<p><img src="../reference/figures/benchmark_2.png"></p>
|
||
<p>That takes up to 8 times as much time! A value of 145 milliseconds means it can only determine ~7 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.</p>
|
||
<p>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 mean that unique values 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_fullname()</a></code> for this test - a helper function that returns the full microbial name (genus, species and possibly subspecies) and uses <code><a href="../reference/as.mo.html">as.mo()</a></code> internally.</p>
|
||
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(dplyr)</a>
|
||
<a class="sourceLine" id="cb4-2" title="2"><span class="co"># take 500,000 random MO codes from the septic_patients data set</span></a>
|
||
<a class="sourceLine" id="cb4-3" title="3">x =<span class="st"> </span>septic_patients <span class="op">%>%</span></a>
|
||
<a class="sourceLine" id="cb4-4" title="4"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/sample.html">sample_n</a></span>(<span class="dv">500000</span>, <span class="dt">replace =</span> <span class="ot">TRUE</span>) <span class="op">%>%</span></a>
|
||
<a class="sourceLine" id="cb4-5" title="5"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/pull.html">pull</a></span>(mo)</a>
|
||
<a class="sourceLine" id="cb4-6" title="6"> </a>
|
||
<a class="sourceLine" id="cb4-7" title="7"><span class="co"># got the right length?</span></a>
|
||
<a class="sourceLine" id="cb4-8" title="8"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/length">length</a></span>(x)</a>
|
||
<a class="sourceLine" id="cb4-9" title="9"><span class="co"># [1] 500000</span></a>
|
||
<a class="sourceLine" id="cb4-10" title="10"></a>
|
||
<a class="sourceLine" id="cb4-11" title="11"><span class="co"># and how many unique values do we have?</span></a>
|
||
<a class="sourceLine" id="cb4-12" title="12"><span class="kw"><a href="https://dplyr.tidyverse.org/reference/n_distinct.html">n_distinct</a></span>(x)</a>
|
||
<a class="sourceLine" id="cb4-13" title="13"><span class="co"># [1] 96</span></a>
|
||
<a class="sourceLine" id="cb4-14" title="14"></a>
|
||
<a class="sourceLine" id="cb4-15" title="15"><span class="co"># only 96, but distributed in 500,000 results. now let's see:</span></a>
|
||
<a class="sourceLine" id="cb4-16" title="16"><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="dt">X =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(x),</a>
|
||
<a class="sourceLine" id="cb4-17" title="17"> <span class="dt">times =</span> <span class="dv">10</span>,</a>
|
||
<a class="sourceLine" id="cb4-18" title="18"> <span class="dt">unit =</span> <span class="st">"ms"</span>)</a>
|
||
<a class="sourceLine" id="cb4-19" title="19"><span class="co"># Unit: milliseconds</span></a>
|
||
<a class="sourceLine" id="cb4-20" title="20"><span class="co"># expr min lq mean median uq max neval</span></a>
|
||
<a class="sourceLine" id="cb4-21" title="21"><span class="co"># X 114.9342 117.1076 129.6448 120.2047 131.5005 168.6371 10</span></a></code></pre></div>
|
||
<p>So transforming 500,000 values (!) of 96 unique values only takes 0.12 seconds (120 ms). You only lose time on your unique input values.</p>
|
||
<p>Results of a tenfold - 5,000,000 values:</p>
|
||
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" title="1"><span class="co"># Unit: milliseconds</span></a>
|
||
<a class="sourceLine" id="cb5-2" title="2"><span class="co"># expr min lq mean median uq max neval</span></a>
|
||
<a class="sourceLine" id="cb5-3" title="3"><span class="co"># X 882.9045 901.3011 1001.677 940.3421 1168.088 1226.846 10</span></a></code></pre></div>
|
||
<p>Even determining the full names of 5 <em>Million</em> values is done within a second.</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_fullname()</a></code>, it almost doesn’t take any time at all (see ‘C’ below):</p>
|
||
<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" title="1"><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_fullname</a></span>(<span class="st">"B_STPHY_AUR"</span>),</a>
|
||
<a class="sourceLine" id="cb6-2" title="2"> <span class="dt">B =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. aureus"</span>),</a>
|
||
<a class="sourceLine" id="cb6-3" title="3"> <span class="dt">C =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"Staphylococcus aureus"</span>),</a>
|
||
<a class="sourceLine" id="cb6-4" title="4"> <span class="dt">times =</span> <span class="dv">10</span>,</a>
|
||
<a class="sourceLine" id="cb6-5" title="5"> <span class="dt">unit =</span> <span class="st">"ms"</span>)</a>
|
||
<a class="sourceLine" id="cb6-6" title="6"><span class="co"># Unit: milliseconds</span></a>
|
||
<a class="sourceLine" id="cb6-7" title="7"><span class="co"># expr min lq mean median uq max neval</span></a>
|
||
<a class="sourceLine" id="cb6-8" title="8"><span class="co"># A 11.364086 11.460537 11.5104799 11.4795330 11.524860 11.818263 10</span></a>
|
||
<a class="sourceLine" id="cb6-9" title="9"><span class="co"># B 11.976454 12.012352 12.1704592 12.0853020 12.210004 12.881737 10</span></a>
|
||
<a class="sourceLine" id="cb6-10" title="10"><span class="co"># C 0.095823 0.102528 0.1167754 0.1153785 0.132629 0.140661 10</span></a></code></pre></div>
|
||
<p>So going from <code><a href="../reference/mo_property.html">mo_fullname("Staphylococcus aureus")</a></code> to <code>"Staphylococcus aureus"</code> takes 0.0001 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="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" title="1"><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="cb7-2" title="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="cb7-3" title="3"> <span class="dt">C =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"Staphylococcus aureus"</span>),</a>
|
||
<a class="sourceLine" id="cb7-4" title="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="cb7-5" title="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="cb7-6" title="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="cb7-7" title="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="cb7-8" title="8"> <span class="dt">H =</span> <span class="kw"><a href="../reference/mo_property.html">mo_subkingdom</a></span>(<span class="st">"Posibacteria"</span>),</a>
|
||
<a class="sourceLine" id="cb7-9" title="9"> <span class="dt">I =</span> <span class="kw"><a href="../reference/mo_property.html">mo_kingdom</a></span>(<span class="st">"Bacteria"</span>),</a>
|
||
<a class="sourceLine" id="cb7-10" title="10"> <span class="dt">times =</span> <span class="dv">10</span>,</a>
|
||
<a class="sourceLine" id="cb7-11" title="11"> <span class="dt">unit =</span> <span class="st">"ms"</span>)</a>
|
||
<a class="sourceLine" id="cb7-12" title="12"><span class="co"># Unit: milliseconds</span></a>
|
||
<a class="sourceLine" id="cb7-13" title="13"><span class="co"># expr min lq mean median uq max neval</span></a>
|
||
<a class="sourceLine" id="cb7-14" title="14"><span class="co"># A 0.105181 0.121314 0.1478538 0.1465265 0.166711 0.211409 10</span></a>
|
||
<a class="sourceLine" id="cb7-15" title="15"><span class="co"># B 0.132558 0.146388 0.1584278 0.1499835 0.164895 0.208477 10</span></a>
|
||
<a class="sourceLine" id="cb7-16" title="16"><span class="co"># C 0.135492 0.160355 0.2341847 0.1884665 0.348857 0.395931 10</span></a>
|
||
<a class="sourceLine" id="cb7-17" title="17"><span class="co"># D 0.109650 0.115727 0.1270481 0.1264130 0.128648 0.168317 10</span></a>
|
||
<a class="sourceLine" id="cb7-18" title="18"><span class="co"># E 0.081574 0.096940 0.0992582 0.0980915 0.101479 0.120477 10</span></a>
|
||
<a class="sourceLine" id="cb7-19" title="19"><span class="co"># F 0.081575 0.088489 0.0988463 0.0989650 0.103365 0.126482 10</span></a>
|
||
<a class="sourceLine" id="cb7-20" title="20"><span class="co"># G 0.091981 0.095333 0.1043568 0.1001530 0.111327 0.129625 10</span></a>
|
||
<a class="sourceLine" id="cb7-21" title="21"><span class="co"># H 0.092610 0.093169 0.1009135 0.0985455 0.101828 0.120406 10</span></a>
|
||
<a class="sourceLine" id="cb7-22" title="22"><span class="co"># I 0.087371 0.091213 0.1069758 0.0941815 0.109302 0.192831 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 microorganisms (according to ITIS), 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 take a little while longer:</p>
|
||
<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" title="1"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"en"</span>) <span class="co"># or just mo_fullname("CoNS") on an English system</span></a>
|
||
<a class="sourceLine" id="cb8-2" title="2"><span class="co"># "Coagulase Negative Staphylococcus (CoNS)"</span></a>
|
||
<a class="sourceLine" id="cb8-3" title="3"></a>
|
||
<a class="sourceLine" id="cb8-4" title="4"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"fr"</span>) <span class="co"># or just mo_fullname("CoNS") on a French system</span></a>
|
||
<a class="sourceLine" id="cb8-5" title="5"><span class="co"># "Staphylococcus à coagulase négative (CoNS)"</span></a>
|
||
<a class="sourceLine" id="cb8-6" title="6"></a>
|
||
<a class="sourceLine" id="cb8-7" title="7"><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_fullname</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"en"</span>),</a>
|
||
<a class="sourceLine" id="cb8-8" title="8"> <span class="dt">de =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"de"</span>),</a>
|
||
<a class="sourceLine" id="cb8-9" title="9"> <span class="dt">nl =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"nl"</span>),</a>
|
||
<a class="sourceLine" id="cb8-10" title="10"> <span class="dt">es =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"es"</span>),</a>
|
||
<a class="sourceLine" id="cb8-11" title="11"> <span class="dt">it =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"it"</span>),</a>
|
||
<a class="sourceLine" id="cb8-12" title="12"> <span class="dt">fr =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"fr"</span>),</a>
|
||
<a class="sourceLine" id="cb8-13" title="13"> <span class="dt">pt =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"pt"</span>),</a>
|
||
<a class="sourceLine" id="cb8-14" title="14"> <span class="dt">times =</span> <span class="dv">10</span>,</a>
|
||
<a class="sourceLine" id="cb8-15" title="15"> <span class="dt">unit =</span> <span class="st">"ms"</span>)</a>
|
||
<a class="sourceLine" id="cb8-16" title="16"><span class="co"># Unit: milliseconds</span></a>
|
||
<a class="sourceLine" id="cb8-17" title="17"><span class="co"># expr min lq mean median uq max neval</span></a>
|
||
<a class="sourceLine" id="cb8-18" title="18"><span class="co"># en 6.093583 6.51724 6.555105 6.562986 6.630663 6.99698 100</span></a>
|
||
<a class="sourceLine" id="cb8-19" title="19"><span class="co"># de 13.934874 14.35137 16.891587 14.462210 14.764658 43.63956 100</span></a>
|
||
<a class="sourceLine" id="cb8-20" title="20"><span class="co"># nl 13.900092 14.34729 15.943268 14.424565 14.581535 43.76283 100</span></a>
|
||
<a class="sourceLine" id="cb8-21" title="21"><span class="co"># es 13.833813 14.34596 14.574783 14.439757 14.653994 17.49168 100</span></a>
|
||
<a class="sourceLine" id="cb8-22" title="22"><span class="co"># it 13.811883 14.36621 15.179060 14.453515 14.812359 43.64284 100</span></a>
|
||
<a class="sourceLine" id="cb8-23" title="23"><span class="co"># fr 13.798683 14.37019 16.344731 14.468775 14.697610 48.62923 100</span></a>
|
||
<a class="sourceLine" id="cb8-24" title="24"><span class="co"># pt 13.789674 14.36244 15.706321 14.443772 14.679905 44.76701 100</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/c.glasner/">Corinna Glasner</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>.</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>
|