mirror of
https://github.com/msberends/AMR.git
synced 2024-12-27 10:46:12 +01:00
dr. M.S. (Matthijs) Berends
45e9546538
Merge branch 'development' of https://github.com/msberends/AMR into development # Conflicts: # docs/articles/AMR.html # docs/articles/AMR_files/figure-html/disk_plots-1.png # docs/articles/AMR_files/figure-html/disk_plots_mo_ab-1.png # docs/articles/AMR_files/figure-html/mic_plots-1.png # docs/articles/AMR_files/figure-html/mic_plots-2.png # docs/articles/AMR_files/figure-html/mic_plots_mo_ab-1.png # docs/articles/AMR_files/figure-html/mic_plots_mo_ab-2.png # docs/articles/AMR_files/figure-html/plot 1-1.png # docs/articles/AMR_files/figure-html/plot 3-1.png # docs/articles/AMR_files/figure-html/plot 4-1.png # docs/articles/AMR_files/figure-html/plot 5-1.png # docs/articles/EUCAST.html # docs/articles/MDR.html # docs/articles/PCA.html # docs/articles/PCA_files/figure-html/unnamed-chunk-6-1.png # docs/articles/PCA_files/figure-html/unnamed-chunk-7-1.png # docs/articles/SPSS.html # docs/articles/WHONET.html # docs/articles/WHONET_files/figure-html/unnamed-chunk-7-1.png # docs/articles/benchmarks.html # docs/articles/benchmarks_files/figure-html/unnamed-chunk-4-1.png # docs/articles/datasets.html # docs/articles/resistance_predict.html # docs/articles/resistance_predict_files/figure-html/unnamed-chunk-4-1.png # docs/articles/resistance_predict_files/figure-html/unnamed-chunk-5-1.png # docs/articles/resistance_predict_files/figure-html/unnamed-chunk-5-2.png # docs/articles/resistance_predict_files/figure-html/unnamed-chunk-6-1.png # docs/articles/resistance_predict_files/figure-html/unnamed-chunk-7-1.png # docs/articles/welcome_to_AMR.html # docs/news/index.html # docs/pkgdown.yml # docs/reference/AMR-deprecated.html # docs/reference/AMR.html # docs/reference/WHOCC.html # docs/reference/WHONET.html # docs/reference/antibiotics.html # docs/reference/catalogue_of_life.html # docs/reference/catalogue_of_life_version.html # docs/reference/dosage.html # docs/reference/example_isolates.html # docs/reference/example_isolates_unclean.html # docs/reference/g.test.html # docs/reference/intrinsic_resistant.html # docs/reference/microorganisms.codes.html # docs/reference/microorganisms.html # docs/reference/microorganisms.old.html # docs/reference/rsi_translation.html
556 lines
33 KiB
HTML
556 lines
33 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>How to import data from SPSS / SAS / Stata • AMR (for R)</title>
|
||
<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
|
||
<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
|
||
<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
|
||
<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
|
||
<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
|
||
<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
|
||
<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
|
||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css">
|
||
<script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
|
||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous">
|
||
<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet">
|
||
<script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet">
|
||
<script src="../extra.js"></script><meta property="og:title" content="How to import data from SPSS / SAS / Stata">
|
||
<meta property="og:description" content="AMR">
|
||
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg">
|
||
<meta name="twitter:card" content="summary_large_image">
|
||
<meta name="twitter:creator" content="@msberends">
|
||
<meta name="twitter:site" content="@univgroningen">
|
||
<!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
|
||
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
|
||
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
|
||
<![endif]-->
|
||
</head>
|
||
<body data-spy="scroll" data-target="#toc">
|
||
|
||
|
||
<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>
|
||
<<<<<<< HEAD
|
||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
|
||
=======
|
||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
|
||
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
|
||
</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/datasets.html">
|
||
<span class="fa fa-database"></span>
|
||
|
||
Data sets for download / own use
|
||
</a>
|
||
</li>
|
||
<li>
|
||
<a href="../articles/PCA.html">
|
||
<span class="fa fa-compress"></span>
|
||
|
||
Conduct principal component analysis for AMR
|
||
</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/index.html">
|
||
<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/index.html">
|
||
<span class="far fa-newspaper"></span>
|
||
|
||
Changelog
|
||
</a>
|
||
</li>
|
||
</ul>
|
||
<ul class="nav navbar-nav navbar-right">
|
||
<li>
|
||
<a href="https://github.com/msberends/AMR" class="external-link">
|
||
<span class="fab fa-github"></span>
|
||
|
||
Source Code
|
||
</a>
|
||
</li>
|
||
</ul>
|
||
</div>
|
||
<!--/.nav-collapse -->
|
||
</div>
|
||
<!--/.container -->
|
||
</div>
|
||
<!--/.navbar -->
|
||
|
||
|
||
|
||
</header><script src="SPSS_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
|
||
<div class="col-md-9 contents">
|
||
<div class="page-header toc-ignore">
|
||
<h1 data-toc-skip>How to import data from SPSS / SAS / Stata</h1>
|
||
<h4 data-toc-skip class="author">Dr. Matthijs
|
||
Berends</h4>
|
||
|
||
<<<<<<< HEAD
|
||
<h4 data-toc-skip class="date">14 March 2022</h4>
|
||
=======
|
||
<h4 data-toc-skip class="date">12 March 2022</h4>
|
||
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
|
||
|
||
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/SPSS.Rmd" class="external-link"><code>vignettes/SPSS.Rmd</code></a></small>
|
||
<div class="hidden name"><code>SPSS.Rmd</code></div>
|
||
|
||
</div>
|
||
|
||
|
||
|
||
<div class="section level2">
|
||
<h2 id="spss-sas-stata">SPSS / SAS / Stata<a class="anchor" aria-label="anchor" href="#spss-sas-stata"></a>
|
||
</h2>
|
||
<p>SPSS (Statistical Package for the Social Sciences) is probably the
|
||
most well-known software package for statistical analysis. SPSS is
|
||
easier to learn than R, because in SPSS you only have to click a menu to
|
||
run parts of your analysis. Because of its user-friendliness, it is
|
||
taught at universities and particularly useful for students who are new
|
||
to statistics. From my experience, I would guess that pretty much all
|
||
(bio)medical students know it at the time they graduate. SAS and Stata
|
||
are comparable statistical packages popular in big industries.</p>
|
||
</div>
|
||
<div class="section level2">
|
||
<h2 id="compared-to-r">Compared to R<a class="anchor" aria-label="anchor" href="#compared-to-r"></a>
|
||
</h2>
|
||
<p>As said, SPSS is easier to learn than R. But SPSS, SAS and Stata come
|
||
with major downsides when comparing it with R:</p>
|
||
<ul>
|
||
<li>
|
||
<p><strong>R is highly modular.</strong></p>
|
||
<p>The <a href="https://cran.r-project.org/" class="external-link">official R network
|
||
(CRAN)</a> features more than 16,000 packages at the time of writing,
|
||
our <code>AMR</code> package being one of them. All these packages were
|
||
peer-reviewed before publication. Aside from this official channel,
|
||
there are also developers who choose not to submit to CRAN, but rather
|
||
keep it on their own public repository, like GitHub. So there may even
|
||
be a lot more than 14,000 packages out there.</p>
|
||
<p>Bottom line is, you can really extend it yourself or ask somebody to
|
||
do this for you. Take for example our <code>AMR</code> package. Among
|
||
other things, it adds reliable reference data to R to help you with the
|
||
data cleaning and analysis. SPSS, SAS and Stata will never know what a
|
||
valid MIC value is or what the Gram stain of <em>E. coli</em> is. Or
|
||
that all species of <em>Klebiella</em> are resistant to amoxicillin and
|
||
that Floxapen<sup>®</sup> is a trade name of flucloxacillin. These facts
|
||
and properties are often needed to clean existing data, which would be
|
||
very inconvenient in a software package without reliable reference data.
|
||
See below for a demonstration.</p>
|
||
</li>
|
||
<li>
|
||
<p><strong>R is extremely flexible.</strong></p>
|
||
<p>Because you write the syntax yourself, you can do anything you want.
|
||
The flexibility in transforming, arranging, grouping and summarising
|
||
data, or drawing plots, is endless - with SPSS, SAS or Stata you are
|
||
bound to their algorithms and format styles. They may be a bit flexible,
|
||
but you can probably never create that very specific publication-ready
|
||
plot without using other (paid) software. If you sometimes write
|
||
syntaxes in SPSS to run a complete analysis or to ‘automate’ some of
|
||
your work, you could do this a lot less time in R. You will notice that
|
||
writing syntaxes in R is a lot more nifty and clever than in SPSS.
|
||
Still, as working with any statistical package, you will have to have
|
||
knowledge about what you are doing (statistically) and what you are
|
||
willing to accomplish.</p>
|
||
</li>
|
||
<li>
|
||
<p><strong>R can be easily automated.</strong></p>
|
||
<p>Over the last years, <a href="https://rmarkdown.rstudio.com/" class="external-link">R
|
||
Markdown</a> has really made an interesting development. With R
|
||
Markdown, you can very easily produce reports, whether the format has to
|
||
be Word, PowerPoint, a website, a PDF document or just the raw data to
|
||
Excel. It even allows the use of a reference file containing the layout
|
||
style (e.g. fonts and colours) of your organisation. I use this a lot to
|
||
generate weekly and monthly reports automatically. Just write the code
|
||
once and enjoy the automatically updated reports at any interval you
|
||
like.</p>
|
||
<p>For an even more professional environment, you could create <a href="https://shiny.rstudio.com/" class="external-link">Shiny apps</a>: live manipulation of
|
||
data using a custom made website. The webdesign knowledge needed
|
||
(JavaScript, CSS, HTML) is almost <em>zero</em>.</p>
|
||
</li>
|
||
<li>
|
||
<p><strong>R has a huge community.</strong></p>
|
||
<<<<<<< HEAD
|
||
<p>Many R users just ask questions on websites like <a href="https://stackoverflow.com" class="external-link">StackOverflow.com</a>, the largest
|
||
online community for programmers. At the time of writing, <a href="https://stackoverflow.com/questions/tagged/r?sort=votes" class="external-link">439,954
|
||
R-related questions</a> have already been asked on this platform (that
|
||
covers questions and answers for any programming language). In my own
|
||
experience, most questions are answered within a couple of
|
||
minutes.</p>
|
||
=======
|
||
<p>Many R users just ask questions on websites like <a href="https://stackoverflow.com" class="external-link">StackOverflow.com</a>, the largest online community for programmers. At the time of writing, <a href="https://stackoverflow.com/questions/tagged/r?sort=votes" class="external-link">439,030 R-related questions</a> have already been asked on this platform (that covers questions and answers for any programming language). In my own experience, most questions are answered within a couple of minutes.</p>
|
||
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
|
||
</li>
|
||
<li>
|
||
<p><strong>R understands any data type, including
|
||
SPSS/SAS/Stata.</strong></p>
|
||
<p>And that’s not vice versa I’m afraid. You can import data from any
|
||
source into R. For example from SPSS, SAS and Stata (<a href="https://haven.tidyverse.org/" class="external-link">link</a>), from Minitab, Epi Info
|
||
and EpiData (<a href="https://cran.r-project.org/package=foreign" class="external-link">link</a>), from Excel
|
||
(<a href="https://readxl.tidyverse.org/" class="external-link">link</a>), from flat files like
|
||
CSV, TXT or TSV (<a href="https://readr.tidyverse.org/" class="external-link">link</a>), or
|
||
directly from databases and datawarehouses from anywhere on the world
|
||
(<a href="https://dbplyr.tidyverse.org/" class="external-link">link</a>). You can even scrape
|
||
websites to download tables that are live on the internet (<a href="https://github.com/hadley/rvest" class="external-link">link</a>) or get the results of
|
||
an API call and transform it into data in only one command (<a href="https://github.com/Rdatatable/data.table/wiki/Convenience-features-of-fread" class="external-link">link</a>).</p>
|
||
<p>And the best part - you can export from R to most data formats as
|
||
well. So you can import an SPSS file, do your analysis neatly in R and
|
||
export the resulting tables to Excel files for sharing.</p>
|
||
</li>
|
||
<li>
|
||
<p><strong>R is completely free and open-source.</strong></p>
|
||
<p>No strings attached. It was created and is being maintained by
|
||
volunteers who believe that (data) science should be open and publicly
|
||
available to everybody. SPSS, SAS and Stata are quite expensive. IBM
|
||
SPSS Staticstics only comes with subscriptions nowadays, varying <a href="https://www.ibm.com/products/spss-statistics/pricing" class="external-link">between USD
|
||
1,300 and USD 8,500</a> per user <em>per year</em>. SAS Analytics Pro
|
||
costs <a href="https://www.sas.com/store/products-solutions/sas-analytics-pro/prodPERSANL.html" class="external-link">around
|
||
USD 10,000</a> per computer. Stata also has a business model with
|
||
subscription fees, varying <a href="https://www.stata.com/order/new/bus/single-user-licenses/dl/" class="external-link">between
|
||
USD 600 and USD 2,800</a> per computer per year, but lower prices come
|
||
with a limitation of the number of variables you can work with. And
|
||
still they do not offer the above benefits of R.</p>
|
||
<p>If you are working at a midsized or small company, you can save it
|
||
tens of thousands of dollars by using R instead of e.g. SPSS - gaining
|
||
even more functions and flexibility. And all R enthousiasts can do as
|
||
much PR as they want (like I do here), because nobody is officially
|
||
associated with or affiliated by R. It is really free.</p>
|
||
</li>
|
||
<li>
|
||
<<<<<<< HEAD
|
||
<p><strong>R is (nowadays) the preferred analysis software in
|
||
academic papers.</strong></p>
|
||
<p>At present, R is among the world most powerful statistical languages,
|
||
and it is generally very popular in science (Bollmann <em>et al.</em>,
|
||
2017). For all the above reasons, the number of references to R as an
|
||
analysis method in academic papers <a href="https://r4stats.com/2014/08/20/r-passes-spss-in-scholarly-use-stata-growing-rapidly/" class="external-link">is
|
||
rising continuously</a> and has even surpassed SPSS for academic use
|
||
(Muenchen, 2014).</p>
|
||
<p>I believe that the thing with SPSS is, that it has always had a great
|
||
user interface which is very easy to learn and use. Back when they
|
||
developed it, they had very little competition, let alone from R. R
|
||
didn’t even had a professional user interface until the last decade
|
||
(called RStudio, see below). How people used R between the nineties and
|
||
2010 is almost completely incomparable to how R is being used now. The
|
||
language itself <a href="https://www.tidyverse.org/packages/" class="external-link">has been
|
||
restyled completely</a> by volunteers who are dedicated professionals in
|
||
the field of data science. SPSS was great when there was nothing else
|
||
that could compete. But now in 2022, I don’t see any reason why SPSS
|
||
would be of any better use than R.</p>
|
||
=======
|
||
<p><strong>R is (nowadays) the preferred analysis software in academic papers.</strong></p>
|
||
<p>At present, R is among the world most powerful statistical languages, and it is generally very popular in science (Bollmann <em>et al.</em>, 2017). For all the above reasons, the number of references to R as an analysis method in academic papers <a href="https://r4stats.com/2014/08/20/r-passes-spss-in-scholarly-use-stata-growing-rapidly/" class="external-link">is rising continuously</a> and has even surpassed SPSS for academic use (Muenchen, 2014).</p>
|
||
<p>I believe that the thing with SPSS is, that it has always had a great user interface which is very easy to learn and use. Back when they developed it, they had very little competition, let alone from R. R didn’t even had a professional user interface until the last decade (called RStudio, see below). How people used R between the nineties and 2010 is almost completely incomparable to how R is being used now. The language itself <a href="https://www.tidyverse.org/packages/" class="external-link">has been restyled completely</a> by volunteers who are dedicated professionals in the field of data science. SPSS was great when there was nothing else that could compete. But now in 2022, I don’t see any reason why SPSS would be of any better use than R.</p>
|
||
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
|
||
</li>
|
||
</ul>
|
||
<p>To demonstrate the first point:</p>
|
||
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
|
||
<code class="sourceCode R"><span class="co"># not all values are valid MIC values:</span>
|
||
<span class="fu"><a href="../reference/as.mic.html">as.mic</a></span><span class="op">(</span><span class="fl">0.125</span><span class="op">)</span>
|
||
<span class="co"># Class <mic></span>
|
||
<span class="co"># [1] 0.125</span>
|
||
<span class="fu"><a href="../reference/as.mic.html">as.mic</a></span><span class="op">(</span><span class="st">"testvalue"</span><span class="op">)</span>
|
||
<span class="co"># Class <mic></span>
|
||
<span class="co"># [1] <NA></span>
|
||
|
||
<span class="co"># the Gram stain is available for all bacteria:</span>
|
||
<span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span>
|
||
<span class="co"># [1] "Gram-negative"</span>
|
||
|
||
<span class="co"># Klebsiella is intrinsic resistant to amoxicillin, according to EUCAST:</span>
|
||
<span class="va">klebsiella_test</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>mo <span class="op">=</span> <span class="st">"klebsiella"</span>,
|
||
amox <span class="op">=</span> <span class="st">"S"</span>,
|
||
stringsAsFactors <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>
|
||
<span class="va">klebsiella_test</span> <span class="co"># (our original data)</span>
|
||
<span class="co"># mo amox</span>
|
||
<span class="co"># 1 klebsiella S</span>
|
||
<span class="fu"><a href="../reference/eucast_rules.html">eucast_rules</a></span><span class="op">(</span><span class="va">klebsiella_test</span>, info <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span> <span class="co"># (the edited data by EUCAST rules)</span>
|
||
<span class="co"># mo amox</span>
|
||
<span class="co"># 1 klebsiella R</span>
|
||
|
||
<span class="co"># hundreds of trade names can be translated to a name, trade name or an ATC code:</span>
|
||
<span class="fu"><a href="../reference/ab_property.html">ab_name</a></span><span class="op">(</span><span class="st">"floxapen"</span><span class="op">)</span>
|
||
<span class="co"># [1] "Flucloxacillin"</span>
|
||
<span class="fu"><a href="../reference/ab_property.html">ab_tradenames</a></span><span class="op">(</span><span class="st">"floxapen"</span><span class="op">)</span>
|
||
<span class="co"># [1] "floxacillin" "floxapen" "floxapen sodium salt"</span>
|
||
<span class="co"># [4] "fluclox" "flucloxacilina" "flucloxacillin" </span>
|
||
<span class="co"># [7] "flucloxacilline" "flucloxacillinum" "fluorochloroxacillin"</span>
|
||
<span class="fu"><a href="../reference/ab_property.html">ab_atc</a></span><span class="op">(</span><span class="st">"floxapen"</span><span class="op">)</span>
|
||
<span class="co"># [1] "J01CF05"</span></code></pre></div>
|
||
</div>
|
||
<div class="section level2">
|
||
<h2 id="import-data-from-spsssasstata">Import data from SPSS/SAS/Stata<a class="anchor" aria-label="anchor" href="#import-data-from-spsssasstata"></a>
|
||
</h2>
|
||
<div class="section level3">
|
||
<h3 id="rstudio">RStudio<a class="anchor" aria-label="anchor" href="#rstudio"></a>
|
||
</h3>
|
||
<p>To work with R, probably the best option is to use <a href="https://www.rstudio.com/products/rstudio/" class="external-link">RStudio</a>. It is an
|
||
open-source and free desktop environment which not only allows you to
|
||
run R code, but also supports project management, version management,
|
||
package management and convenient import menus to work with other data
|
||
sources. You can also install <a href="https://www.rstudio.com/products/rstudio/" class="external-link">RStudio Server</a> on a
|
||
private or corporate server, which brings nothing less than the complete
|
||
RStudio software to you as a website (at home or at work).</p>
|
||
<p>To import a data file, just click <em>Import Dataset</em> in the
|
||
Environment tab:</p>
|
||
<p><img src="https://github.com/msberends/AMR/raw/main/docs/import1.png"></p>
|
||
<p>If additional packages are needed, RStudio will ask you if they
|
||
should be installed on beforehand.</p>
|
||
<p>In the the window that opens, you can define all options (parameters)
|
||
that should be used for import and you’re ready to go:</p>
|
||
<p><img src="https://github.com/msberends/AMR/raw/main/docs/import2.png"></p>
|
||
<p>If you want named variables to be imported as factors so it resembles
|
||
SPSS more, use <code><a href="https://haven.tidyverse.org/reference/as_factor.html" class="external-link">as_factor()</a></code>.</p>
|
||
<p>The difference is this:</p>
|
||
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
|
||
<code class="sourceCode R"><span class="va">SPSS_data</span>
|
||
<span class="co"># # A tibble: 4,203 x 4</span>
|
||
<span class="co"># v001 sex status statusage</span>
|
||
<span class="co"># <dbl> <dbl+lbl> <dbl+lbl> <dbl></span>
|
||
<span class="co"># 1 10002 1 1 76.6</span>
|
||
<span class="co"># 2 10004 0 1 59.1</span>
|
||
<span class="co"># 3 10005 1 1 54.5</span>
|
||
<span class="co"># 4 10006 1 1 54.1</span>
|
||
<span class="co"># 5 10007 1 1 57.7</span>
|
||
<span class="co"># 6 10008 1 1 62.8</span>
|
||
<span class="co"># 7 10010 0 1 63.7</span>
|
||
<span class="co"># 8 10011 1 1 73.1</span>
|
||
<span class="co"># 9 10017 1 1 56.7</span>
|
||
<span class="co"># 10 10018 0 1 66.6</span>
|
||
<span class="co"># # ... with 4,193 more rows</span>
|
||
|
||
<span class="fu">as_factor</span><span class="op">(</span><span class="va">SPSS_data</span><span class="op">)</span>
|
||
<span class="co"># # A tibble: 4,203 x 4</span>
|
||
<span class="co"># v001 sex status statusage</span>
|
||
<span class="co"># <dbl> <fct> <fct> <dbl></span>
|
||
<span class="co"># 1 10002 Male alive 76.6</span>
|
||
<span class="co"># 2 10004 Female alive 59.1</span>
|
||
<span class="co"># 3 10005 Male alive 54.5</span>
|
||
<span class="co"># 4 10006 Male alive 54.1</span>
|
||
<span class="co"># 5 10007 Male alive 57.7</span>
|
||
<span class="co"># 6 10008 Male alive 62.8</span>
|
||
<span class="co"># 7 10010 Female alive 63.7</span>
|
||
<span class="co"># 8 10011 Male alive 73.1</span>
|
||
<span class="co"># 9 10017 Male alive 56.7</span>
|
||
<span class="co"># 10 10018 Female alive 66.6</span>
|
||
<span class="co"># # ... with 4,193 more rows</span></code></pre></div>
|
||
</div>
|
||
<div class="section level3">
|
||
<h3 id="base-r">Base R<a class="anchor" aria-label="anchor" href="#base-r"></a>
|
||
</h3>
|
||
<p>To import data from SPSS, SAS or Stata, you can use the <a href="https://haven.tidyverse.org/" class="external-link">great <code>haven</code> package</a>
|
||
yourself:</p>
|
||
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
|
||
<code class="sourceCode R"><span class="co"># download and install the latest version:</span>
|
||
<span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"haven"</span><span class="op">)</span>
|
||
<span class="co"># load the package you just installed:</span>
|
||
<span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://haven.tidyverse.org" class="external-link">haven</a></span><span class="op">)</span> </code></pre></div>
|
||
<p>You can now import files as follows:</p>
|
||
<div class="section level4">
|
||
<h4 id="spss">SPSS<a class="anchor" aria-label="anchor" href="#spss"></a>
|
||
</h4>
|
||
<p>To read files from SPSS into R:</p>
|
||
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
|
||
<code class="sourceCode R"><span class="co"># read any SPSS file based on file extension (best way):</span>
|
||
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_spss.html" class="external-link">read_spss</a></span><span class="op">(</span>file <span class="op">=</span> <span class="st">"path/to/file"</span><span class="op">)</span>
|
||
|
||
<span class="co"># read .sav or .zsav file:</span>
|
||
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_spss.html" class="external-link">read_sav</a></span><span class="op">(</span>file <span class="op">=</span> <span class="st">"path/to/file"</span><span class="op">)</span>
|
||
|
||
<span class="co"># read .por file:</span>
|
||
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_spss.html" class="external-link">read_por</a></span><span class="op">(</span>file <span class="op">=</span> <span class="st">"path/to/file"</span><span class="op">)</span></code></pre></div>
|
||
<p>Do not forget about <code><a href="https://haven.tidyverse.org/reference/as_factor.html" class="external-link">as_factor()</a></code>, as mentioned above.</p>
|
||
<p>To export your R objects to the SPSS file format:</p>
|
||
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
|
||
<code class="sourceCode R"><span class="co"># save as .sav file:</span>
|
||
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_spss.html" class="external-link">write_sav</a></span><span class="op">(</span>data <span class="op">=</span> <span class="va">yourdata</span>, path <span class="op">=</span> <span class="st">"path/to/file"</span><span class="op">)</span>
|
||
|
||
<span class="co"># save as compressed .zsav file:</span>
|
||
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_spss.html" class="external-link">write_sav</a></span><span class="op">(</span>data <span class="op">=</span> <span class="va">yourdata</span>, path <span class="op">=</span> <span class="st">"path/to/file"</span>, compress <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div>
|
||
</div>
|
||
<div class="section level4">
|
||
<h4 id="sas">SAS<a class="anchor" aria-label="anchor" href="#sas"></a>
|
||
</h4>
|
||
<p>To read files from SAS into R:</p>
|
||
<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
|
||
<code class="sourceCode R"><span class="co"># read .sas7bdat + .sas7bcat files:</span>
|
||
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_sas.html" class="external-link">read_sas</a></span><span class="op">(</span>data_file <span class="op">=</span> <span class="st">"path/to/file"</span>, catalog_file <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span>
|
||
|
||
<span class="co"># read SAS transport files (version 5 and version 8):</span>
|
||
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_xpt.html" class="external-link">read_xpt</a></span><span class="op">(</span>file <span class="op">=</span> <span class="st">"path/to/file"</span><span class="op">)</span></code></pre></div>
|
||
<p>To export your R objects to the SAS file format:</p>
|
||
<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
|
||
<code class="sourceCode R"><span class="co"># save as regular SAS file:</span>
|
||
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_sas.html" class="external-link">write_sas</a></span><span class="op">(</span>data <span class="op">=</span> <span class="va">yourdata</span>, path <span class="op">=</span> <span class="st">"path/to/file"</span><span class="op">)</span>
|
||
|
||
<span class="co"># the SAS transport format is an open format </span>
|
||
<span class="co"># (required for submission of the data to the FDA)</span>
|
||
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_xpt.html" class="external-link">write_xpt</a></span><span class="op">(</span>data <span class="op">=</span> <span class="va">yourdata</span>, path <span class="op">=</span> <span class="st">"path/to/file"</span>, version <span class="op">=</span> <span class="fl">8</span><span class="op">)</span></code></pre></div>
|
||
</div>
|
||
<div class="section level4">
|
||
<h4 id="stata">Stata<a class="anchor" aria-label="anchor" href="#stata"></a>
|
||
</h4>
|
||
<p>To read files from Stata into R:</p>
|
||
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
|
||
<code class="sourceCode R"><span class="co"># read .dta file:</span>
|
||
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_dta.html" class="external-link">read_stata</a></span><span class="op">(</span>file <span class="op">=</span> <span class="st">"/path/to/file"</span><span class="op">)</span>
|
||
|
||
<span class="co"># works exactly the same:</span>
|
||
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_dta.html" class="external-link">read_dta</a></span><span class="op">(</span>file <span class="op">=</span> <span class="st">"/path/to/file"</span><span class="op">)</span></code></pre></div>
|
||
<p>To export your R objects to the Stata file format:</p>
|
||
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
|
||
<code class="sourceCode R"><span class="co"># save as .dta file, Stata version 14:</span>
|
||
<span class="co"># (supports Stata v8 until v15 at the time of writing)</span>
|
||
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_dta.html" class="external-link">write_dta</a></span><span class="op">(</span>data <span class="op">=</span> <span class="va">yourdata</span>, path <span class="op">=</span> <span class="st">"/path/to/file"</span>, version <span class="op">=</span> <span class="fl">14</span><span class="op">)</span></code></pre></div>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
|
||
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
|
||
|
||
<nav id="toc" data-toggle="toc"><h2 data-toc-skip>Contents</h2>
|
||
</nav>
|
||
</div>
|
||
|
||
</div>
|
||
|
||
|
||
|
||
<footer><div class="copyright">
|
||
<p></p>
|
||
<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||
Erwin E. A. Hassing.</p>
|
||
</div>
|
||
|
||
<div class="pkgdown">
|
||
<p></p>
|
||
<<<<<<< HEAD
|
||
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
||
2.0.2.</p>
|
||
=======
|
||
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
|
||
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
|
||
</div>
|
||
|
||
</footer>
|
||
</div>
|
||
|
||
|
||
|
||
|
||
|
||
|
||
</body>
|
||
</html>
|