AMR/docs/reference/mo_source.html

373 lines
15 KiB
HTML
Raw Normal View History

2019-01-21 15:53:01 +01:00
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
<html lang="en">
<head>
<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>Use predefined reference data set — mo_source • 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" />
2019-10-13 09:31:58 +02:00
2019-01-21 15:53:01 +01:00
<!-- 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" />
2019-10-13 09:31:58 +02:00
2019-01-21 15:53:01 +01:00
<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 -->
2019-10-13 09:31:58 +02:00
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
2019-01-21 15:53:01 +01:00
<!-- 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>
2019-10-13 09:31:58 +02:00
<!-- headroom.js -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
2019-01-21 15:53:01 +01:00
<!-- 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>
2019-10-13 09:31:58 +02:00
<meta property="og:title" content="Use predefined reference data set — mo_source" />
2019-02-28 13:56:28 +01:00
<meta property="og:description" content="These functions can be used to predefine your own reference to be used in as.mo and consequently all mo_* functions like mo_genus and mo_gramstain.
This is the fastest way to have your organisation (or analysis) specific codes picked up and translated by this package." />
2019-01-21 15:53:01 +01:00
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
<meta name="twitter:card" content="summary" />
2019-10-13 09:31:58 +02:00
2019-01-21 15:53:01 +01:00
<!-- 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]-->
2019-10-13 09:31:58 +02:00
2019-01-21 15:53:01 +01:00
</head>
<body>
<div class="container template-reference-topic">
<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">0.8.0.9032</span>
2019-01-21 15:53:01 +01:00
</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>
2019-02-14 10:23:51 +01:00
<a href="../articles/resistance_predict.html">
2019-01-21 15:53:01 +01:00
<span class="fa fa-dice"></span>
Predict antimicrobial resistance
</a>
</li>
2019-05-28 16:50:40 +02:00
<li>
<a href="../articles/MDR.html">
<span class="fa fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
</a>
</li>
2019-01-29 00:06:50 +01:00
<li>
<a href="../articles/WHONET.html">
<span class="fa fa-globe-americas"></span>
Work with WHONET data
</a>
</li>
2019-02-14 15:18:17 +01:00
<li>
<a href="../articles/SPSS.html">
<span class="fa fa-file-upload"></span>
Import data from SPSS/SAS/Stata
</a>
</li>
2019-01-21 15:53:01 +01:00
<li>
<a href="../articles/EUCAST.html">
<span class="fa fa-exchange-alt"></span>
Apply EUCAST rules
</a>
</li>
<li>
2019-02-14 10:23:51 +01:00
<a href="../reference/mo_property.html">
2019-01-21 15:53:01 +01:00
<span class="fa fa-bug"></span>
Get properties of a microorganism
</a>
</li>
<li>
2019-05-16 21:20:00 +02:00
<a href="../reference/ab_property.html">
2019-01-21 15:53:01 +01:00
<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>
2019-10-13 09:31:58 +02:00
<form class="navbar-form navbar-right hidden-xs hidden-sm" role="search">
2019-01-21 15:53:01 +01:00
<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 -->
2019-10-13 09:31:58 +02:00
2019-01-21 15:53:01 +01:00
</header>
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Use predefined reference data set</h1>
<div class="hidden name"><code>mo_source.Rd</code></div>
</div>
<div class="ref-description">
<p>These functions can be used to predefine your own reference to be used in <code><a href='as.mo.html'>as.mo</a></code> and consequently all <code>mo_*</code> functions like <code><a href='mo_property.html'>mo_genus</a></code> and <code><a href='mo_property.html'>mo_gramstain</a></code>.</p>
2019-02-28 13:56:28 +01:00
<p>This is <strong>the fastest way</strong> to have your organisation (or analysis) specific codes picked up and translated by this package.</p>
2019-01-21 15:53:01 +01:00
</div>
<pre class="usage"><span class='fu'>set_mo_source</span>(<span class='no'>path</span>)
<span class='fu'>get_mo_source</span>()</pre>
2019-10-13 09:31:58 +02:00
2019-01-21 15:53:01 +01:00
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>path</th>
<td><p>location of your reference file, see Details</p></td>
</tr>
</table>
2019-10-13 09:31:58 +02:00
2019-01-21 15:53:01 +01:00
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
2019-02-27 11:36:12 +01:00
<p>The reference file can be a text file seperated with commas (CSV) or tabs or pipes, an Excel file (either 'xls' or 'xlsx' format) or an R object file (extension '.rds'). To use an Excel file, you need to have the <code>readxl</code> package installed.</p>
2019-10-13 09:31:58 +02:00
<p><code>set_mo_source</code> will check the file for validity: it must be a <code>data.frame</code>, must have a column named <code>"mo"</code> which contains values from <code>microorganisms$mo</code> and must have a reference column with your own defined values. If all tests pass, <code>set_mo_source</code> will read the file into R and export it to <code>"~/.mo_source.rds"</code>. This compressed data file will then be used at default for MO determination (function <code><a href='as.mo.html'>as.mo</a></code> and consequently all <code>mo_*</code> functions like <code><a href='mo_property.html'>mo_genus</a></code> and <code><a href='mo_property.html'>mo_gramstain</a></code>). The location of the original file will be saved as option with <code><a href='https://rdrr.io/r/base/options.html'>options</a>(mo_source = path)</code>. Its timestamp will be saved with <code><a href='https://rdrr.io/r/base/options.html'>options</a>(mo_source_datetime = ...)</code>.</p>
<p><code>get_mo_source</code> will return the data set by reading <code>"~/.mo_source.rds"</code> with <code><a href='https://rdrr.io/r/base/readRDS.html'>readRDS</a></code>. If the original file has changed (the file defined with <code>path</code>), it will call <code>set_mo_source</code> to update the data file automatically.</p>
2019-02-27 11:36:12 +01:00
<p>Reading an Excel file (<code>.xlsx</code>) with only one row has a size of 8-9 kB. The compressed file used by this package will have a size of 0.1 kB and can be read by <code>get_mo_source</code> in only a couple of microseconds (a millionth of a second).</p>
2019-02-28 13:56:28 +01:00
<h2 class="hasAnchor" id="how-it-works"><a class="anchor" href="#how-it-works"></a>How it works</h2>
2019-10-13 09:31:58 +02:00
<p>Imagine this data on a sheet of an Excel file (mo codes were looked up in the `microorganisms` data set). The first column contains the organisation specific codes, the second column contains an MO code from this package:</p><pre>
2019-02-28 13:56:28 +01:00
| A | B |
--|--------------------|-------------|
1 | Organisation XYZ | mo |
2 | lab_mo_ecoli | B_ESCHR_COL |
3 | lab_mo_kpneumoniae | B_KLBSL_PNE |
4 | | |
</pre>
2019-10-13 09:31:58 +02:00
<p>We save it as <code>'home/me/ourcodes.xlsx'</code>. Now we have to set it as a source:</p><pre>
2019-02-28 13:56:28 +01:00
set_mo_source("home/me/ourcodes.xlsx")
# Created mo_source file '~/.mo_source.rds' from 'home/me/ourcodes.xlsx'.
</pre>
2019-10-13 09:31:58 +02:00
<p>It has now created a file "~/.mo_source.rds" with the contents of our Excel file, but only the first column with foreign values and the 'mo' column will be kept.</p>
2019-02-28 13:56:28 +01:00
<p>And now we can use it in our functions:</p><pre>
as.mo("lab_mo_ecoli")
2019-03-01 09:34:04 +01:00
[1] B_ESCHR_COL
2019-10-13 09:31:58 +02:00
mo_genus("lab_mo_kpneumoniae")
2019-03-01 09:34:04 +01:00
[1] "Klebsiella"
2019-10-13 09:31:58 +02:00
# other input values still work too
2019-03-01 09:34:04 +01:00
as.mo(c("Escherichia coli", "E. coli", "lab_mo_ecoli"))
[1] B_ESCHR_COL B_ESCHR_COL B_ESCHR_COL
2019-02-28 13:56:28 +01:00
</pre>
2019-10-13 09:31:58 +02:00
<p>If we edit the Excel file to, let's say, this:</p><pre>
2019-02-28 13:56:28 +01:00
| A | B |
--|--------------------|-------------|
1 | Organisation XYZ | mo |
2 | lab_mo_ecoli | B_ESCHR_COL |
3 | lab_mo_kpneumoniae | B_KLBSL_PNE |
4 | lab_Staph_aureus | B_STPHY_AUR |
5 | | |
</pre>
2019-10-13 09:31:58 +02:00
<p>...any new usage of an MO function in this package will update your data:</p><pre>
2019-02-28 13:56:28 +01:00
as.mo("lab_mo_ecoli")
# Updated mo_source file '~/.mo_source.rds' from 'home/me/ourcodes.xlsx'.
2019-03-01 09:34:04 +01:00
[1] B_ESCHR_COL
2019-10-13 09:31:58 +02:00
mo_genus("lab_Staph_aureus")
2019-03-01 09:34:04 +01:00
[1] "Staphylococcus"
2019-02-28 13:56:28 +01:00
</pre>
2019-10-13 09:31:58 +02:00
<p>To remove the reference completely, just use any of these:</p><pre>
2019-02-28 13:56:28 +01:00
set_mo_source("")
set_mo_source(NULL)
# Removed mo_source file '~/.mo_source.rds'.
</pre>
2019-10-13 09:31:58 +02:00
2019-01-21 15:53:01 +01:00
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
2019-10-13 09:31:58 +02:00
<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
2019-01-21 15:53:01 +01:00
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#details">Details</a></li>
2019-02-28 13:56:28 +01:00
<li><a href="#how-it-works">How it works</a></li>
2019-01-21 15:53:01 +01:00
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
2019-10-13 09:31:58 +02:00
</ul>
2019-01-21 15:53:01 +01:00
</div>
</div>
2019-10-13 09:31:58 +02:00
2019-01-21 15:53:01 +01:00
<footer>
<div class="copyright">
2019-10-13 09:31:58 +02:00
<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>
2019-01-21 15:53:01 +01:00
</div>
<div class="pkgdown">
2019-10-13 09:31:58 +02:00
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
2019-01-21 15:53:01 +01:00
</div>
2019-10-13 09:31:58 +02:00
2019-01-21 15:53:01 +01:00
</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>
2019-10-13 09:31:58 +02:00
2019-01-21 15:53:01 +01:00
</body>
</html>
2019-10-13 09:31:58 +02:00