P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-09 00:43:00 +02:00
Code Releases Activity

(v1.0.1) v 1.0.1

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2020-02-23 20:56:11 +01:00
parent 0d5e78b2cf
commit f444c24ed3
69 changed files with 773 additions and 1042 deletions
Download Patch File Download Diff File Expand all files Collapse all files

233
docs/articles/SPSS.html
View File

@ -16,9 +16,7 @@
<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/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">
<!-- 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><!-- 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><!-- 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="../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="">
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png">
@ -41,7 +39,7 @@
</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">0.9.0.9013</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1</span>
</span>
</div>
@ -166,13 +164,7 @@
</a>
</li>
</ul>
<form class="navbar-form navbar-right hidden-xs hidden-sm" 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 -->
@ -187,7 +179,7 @@
<h1>How to import data from SPSS / SAS / Stata</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">26 January 2020</h4>
<h4 class="date">23 February 2020</h4>
<div class="hidden name"><code>SPSS.Rmd</code></div>
@ -241,39 +233,39 @@
</li>
</ul>
<p>To demonstrate the first point:</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="co"># not all values are valid MIC values:</span></a>
<a class="sourceLine" id="cb1-2" data-line-number="2"><span class="kw"><a href="../reference/as.mic.html">as.mic</a></span>(<span class="fl">0.125</span>)</a>
<a class="sourceLine" id="cb1-3" data-line-number="3"><span class="co"># Class 'mic'</span></a>
<a class="sourceLine" id="cb1-4" data-line-number="4"><span class="co"># [1] 0.125</span></a>
<a class="sourceLine" id="cb1-5" data-line-number="5"><span class="kw"><a href="../reference/as.mic.html">as.mic</a></span>(<span class="st">"testvalue"</span>)</a>
<a class="sourceLine" id="cb1-6" data-line-number="6"><span class="co"># Class 'mic'</span></a>
<a class="sourceLine" id="cb1-7" data-line-number="7"><span class="co"># [1] &lt;NA&gt;</span></a>
<a class="sourceLine" id="cb1-8" data-line-number="8"></a>
<a class="sourceLine" id="cb1-9" data-line-number="9"><span class="co"># the Gram stain is avaiable for all bacteria:</span></a>
<a class="sourceLine" id="cb1-10" data-line-number="10"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>)</a>
<a class="sourceLine" id="cb1-11" data-line-number="11"><span class="co"># [1] "Gram-negative"</span></a>
<a class="sourceLine" id="cb1-12" data-line-number="12"></a>
<a class="sourceLine" id="cb1-13" data-line-number="13"><span class="co"># Klebsiella is intrinsic resistant to amoxicllin, according to EUCAST:</span></a>
<a class="sourceLine" id="cb1-14" data-line-number="14">klebsiella_test &lt;-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span>(<span class="dt">mo =</span> <span class="st">"klebsiella"</span>, </a>
<a class="sourceLine" id="cb1-15" data-line-number="15"> <span class="dt">amox =</span> <span class="st">"S"</span>,</a>
<a class="sourceLine" id="cb1-16" data-line-number="16"> <span class="dt">stringsAsFactors =</span> <span class="ot">FALSE</span>)</a>
<a class="sourceLine" id="cb1-17" data-line-number="17">klebsiella_test <span class="co"># (our original data)</span></a>
<a class="sourceLine" id="cb1-18" data-line-number="18"><span class="co"># mo amox</span></a>
<a class="sourceLine" id="cb1-19" data-line-number="19"><span class="co"># 1 klebsiella S</span></a>
<a class="sourceLine" id="cb1-20" data-line-number="20"><span class="kw"><a href="../reference/eucast_rules.html">eucast_rules</a></span>(klebsiella_test, <span class="dt">info =</span> <span class="ot">FALSE</span>) <span class="co"># (the edited data by EUCAST rules)</span></a>
<a class="sourceLine" id="cb1-21" data-line-number="21"><span class="co"># mo amox</span></a>
<a class="sourceLine" id="cb1-22" data-line-number="22"><span class="co"># 1 klebsiella R</span></a>
<a class="sourceLine" id="cb1-23" data-line-number="23"></a>
<a class="sourceLine" id="cb1-24" data-line-number="24"><span class="co"># hundreds of trade names can be translated to a name, trade name or an ATC code:</span></a>
<a class="sourceLine" id="cb1-25" data-line-number="25"><span class="kw"><a href="../reference/ab_property.html">ab_name</a></span>(<span class="st">"floxapen"</span>)</a>
<a class="sourceLine" id="cb1-26" data-line-number="26"><span class="co"># [1] "Flucloxacillin"</span></a>
<a class="sourceLine" id="cb1-27" data-line-number="27"><span class="kw"><a href="../reference/ab_property.html">ab_tradenames</a></span>(<span class="st">"floxapen"</span>)</a>
<a class="sourceLine" id="cb1-28" data-line-number="28"><span class="co"># [1] "Floxacillin" "FLOXACILLIN" "Floxapen" </span></a>
<a class="sourceLine" id="cb1-29" data-line-number="29"><span class="co"># [4] "Floxapen sodium salt" "Fluclox" "Flucloxacilina" </span></a>
<a class="sourceLine" id="cb1-30" data-line-number="30"><span class="co"># [7] "Flucloxacillin" "Flucloxacilline" "Flucloxacillinum" </span></a>
<a class="sourceLine" id="cb1-31" data-line-number="31"><span class="co"># [10] "Fluorochloroxacillin"</span></a>
<a class="sourceLine" id="cb1-32" data-line-number="32"><span class="kw"><a href="../reference/ab_property.html">ab_atc</a></span>(<span class="st">"floxapen"</span>)</a>
<a class="sourceLine" id="cb1-33" data-line-number="33"><span class="co"># [1] "J01CF05"</span></a></code></pre></div>
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1"></a><span class="co"># not all values are valid MIC values:</span></span>
<span id="cb1-2"><a href="#cb1-2"></a><span class="kw"><a href="../reference/as.mic.html">as.mic</a></span>(<span class="fl">0.125</span>)</span>
<span id="cb1-3"><a href="#cb1-3"></a><span class="co"># Class 'mic'</span></span>
<span id="cb1-4"><a href="#cb1-4"></a><span class="co"># [1] 0.125</span></span>
<span id="cb1-5"><a href="#cb1-5"></a><span class="kw"><a href="../reference/as.mic.html">as.mic</a></span>(<span class="st">"testvalue"</span>)</span>
<span id="cb1-6"><a href="#cb1-6"></a><span class="co"># Class 'mic'</span></span>
<span id="cb1-7"><a href="#cb1-7"></a><span class="co"># [1] &lt;NA&gt;</span></span>
<span id="cb1-8"><a href="#cb1-8"></a></span>
<span id="cb1-9"><a href="#cb1-9"></a><span class="co"># the Gram stain is avaiable for all bacteria:</span></span>
<span id="cb1-10"><a href="#cb1-10"></a><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>)</span>
<span id="cb1-11"><a href="#cb1-11"></a><span class="co"># [1] "Gram-negative"</span></span>
<span id="cb1-12"><a href="#cb1-12"></a></span>
<span id="cb1-13"><a href="#cb1-13"></a><span class="co"># Klebsiella is intrinsic resistant to amoxicllin, according to EUCAST:</span></span>
<span id="cb1-14"><a href="#cb1-14"></a>klebsiella_test &lt;-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span>(<span class="dt">mo =</span> <span class="st">"klebsiella"</span>, </span>
<span id="cb1-15"><a href="#cb1-15"></a> <span class="dt">amox =</span> <span class="st">"S"</span>,</span>
<span id="cb1-16"><a href="#cb1-16"></a> <span class="dt">stringsAsFactors =</span> <span class="ot">FALSE</span>)</span>
<span id="cb1-17"><a href="#cb1-17"></a>klebsiella_test <span class="co"># (our original data)</span></span>
<span id="cb1-18"><a href="#cb1-18"></a><span class="co"># mo amox</span></span>
<span id="cb1-19"><a href="#cb1-19"></a><span class="co"># 1 klebsiella S</span></span>
<span id="cb1-20"><a href="#cb1-20"></a><span class="kw"><a href="../reference/eucast_rules.html">eucast_rules</a></span>(klebsiella_test, <span class="dt">info =</span> <span class="ot">FALSE</span>) <span class="co"># (the edited data by EUCAST rules)</span></span>
<span id="cb1-21"><a href="#cb1-21"></a><span class="co"># mo amox</span></span>
<span id="cb1-22"><a href="#cb1-22"></a><span class="co"># 1 klebsiella R</span></span>
<span id="cb1-23"><a href="#cb1-23"></a></span>
<span id="cb1-24"><a href="#cb1-24"></a><span class="co"># hundreds of trade names can be translated to a name, trade name or an ATC code:</span></span>
<span id="cb1-25"><a href="#cb1-25"></a><span class="kw"><a href="../reference/ab_property.html">ab_name</a></span>(<span class="st">"floxapen"</span>)</span>
<span id="cb1-26"><a href="#cb1-26"></a><span class="co"># [1] "Flucloxacillin"</span></span>
<span id="cb1-27"><a href="#cb1-27"></a><span class="kw"><a href="../reference/ab_property.html">ab_tradenames</a></span>(<span class="st">"floxapen"</span>)</span>
<span id="cb1-28"><a href="#cb1-28"></a><span class="co"># [1] "Floxacillin" "FLOXACILLIN" "Floxapen" </span></span>
<span id="cb1-29"><a href="#cb1-29"></a><span class="co"># [4] "Floxapen sodium salt" "Fluclox" "Flucloxacilina" </span></span>
<span id="cb1-30"><a href="#cb1-30"></a><span class="co"># [7] "Flucloxacillin" "Flucloxacilline" "Flucloxacillinum" </span></span>
<span id="cb1-31"><a href="#cb1-31"></a><span class="co"># [10] "Fluorochloroxacillin"</span></span>
<span id="cb1-32"><a href="#cb1-32"></a><span class="kw"><a href="../reference/ab_property.html">ab_atc</a></span>(<span class="st">"floxapen"</span>)</span>
<span id="cb1-33"><a href="#cb1-33"></a><span class="co"># [1] "J01CF05"</span></span></code></pre></div>
</div>
<div id="import-data-from-spsssasstata" class="section level2">
<h2 class="hasAnchor">
@ -289,97 +281,97 @@
<p><img src="https://gitlab.com/msberends/AMR/raw/master/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">as_factor()</a></code>.</p>
<p>The difference is this:</p>
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" data-line-number="1">SPSS_data</a>
<a class="sourceLine" id="cb2-2" data-line-number="2"><span class="co"># # A tibble: 4,203 x 4</span></a>
<a class="sourceLine" id="cb2-3" data-line-number="3"><span class="co"># v001 sex status statusage</span></a>
<a class="sourceLine" id="cb2-4" data-line-number="4"><span class="co"># &lt;dbl&gt; &lt;dbl+lbl&gt; &lt;dbl+lbl&gt; &lt;dbl&gt;</span></a>
<a class="sourceLine" id="cb2-5" data-line-number="5"><span class="co"># 1 10002 1 1 76.6</span></a>
<a class="sourceLine" id="cb2-6" data-line-number="6"><span class="co"># 2 10004 0 1 59.1</span></a>
<a class="sourceLine" id="cb2-7" data-line-number="7"><span class="co"># 3 10005 1 1 54.5</span></a>
<a class="sourceLine" id="cb2-8" data-line-number="8"><span class="co"># 4 10006 1 1 54.1</span></a>
<a class="sourceLine" id="cb2-9" data-line-number="9"><span class="co"># 5 10007 1 1 57.7</span></a>
<a class="sourceLine" id="cb2-10" data-line-number="10"><span class="co"># 6 10008 1 1 62.8</span></a>
<a class="sourceLine" id="cb2-11" data-line-number="11"><span class="co"># 7 10010 0 1 63.7</span></a>
<a class="sourceLine" id="cb2-12" data-line-number="12"><span class="co"># 8 10011 1 1 73.1</span></a>
<a class="sourceLine" id="cb2-13" data-line-number="13"><span class="co"># 9 10017 1 1 56.7</span></a>
<a class="sourceLine" id="cb2-14" data-line-number="14"><span class="co"># 10 10018 0 1 66.6</span></a>
<a class="sourceLine" id="cb2-15" data-line-number="15"><span class="co"># # … with 4,193 more rows</span></a>
<a class="sourceLine" id="cb2-16" data-line-number="16"></a>
<a class="sourceLine" id="cb2-17" data-line-number="17"><span class="kw">as_factor</span>(SPSS_data)</a>
<a class="sourceLine" id="cb2-18" data-line-number="18"><span class="co"># # A tibble: 4,203 x 4</span></a>
<a class="sourceLine" id="cb2-19" data-line-number="19"><span class="co"># v001 sex status statusage</span></a>
<a class="sourceLine" id="cb2-20" data-line-number="20"><span class="co"># &lt;dbl&gt; &lt;fct&gt; &lt;fct&gt; &lt;dbl&gt;</span></a>
<a class="sourceLine" id="cb2-21" data-line-number="21"><span class="co"># 1 10002 Male alive 76.6</span></a>
<a class="sourceLine" id="cb2-22" data-line-number="22"><span class="co"># 2 10004 Female alive 59.1</span></a>
<a class="sourceLine" id="cb2-23" data-line-number="23"><span class="co"># 3 10005 Male alive 54.5</span></a>
<a class="sourceLine" id="cb2-24" data-line-number="24"><span class="co"># 4 10006 Male alive 54.1</span></a>
<a class="sourceLine" id="cb2-25" data-line-number="25"><span class="co"># 5 10007 Male alive 57.7</span></a>
<a class="sourceLine" id="cb2-26" data-line-number="26"><span class="co"># 6 10008 Male alive 62.8</span></a>
<a class="sourceLine" id="cb2-27" data-line-number="27"><span class="co"># 7 10010 Female alive 63.7</span></a>
<a class="sourceLine" id="cb2-28" data-line-number="28"><span class="co"># 8 10011 Male alive 73.1</span></a>
<a class="sourceLine" id="cb2-29" data-line-number="29"><span class="co"># 9 10017 Male alive 56.7</span></a>
<a class="sourceLine" id="cb2-30" data-line-number="30"><span class="co"># 10 10018 Female alive 66.6</span></a>
<a class="sourceLine" id="cb2-31" data-line-number="31"><span class="co"># # … with 4,193 more rows</span></a></code></pre></div>
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1"></a>SPSS_data</span>
<span id="cb2-2"><a href="#cb2-2"></a><span class="co"># # A tibble: 4,203 x 4</span></span>
<span id="cb2-3"><a href="#cb2-3"></a><span class="co"># v001 sex status statusage</span></span>
<span id="cb2-4"><a href="#cb2-4"></a><span class="co"># &lt;dbl&gt; &lt;dbl+lbl&gt; &lt;dbl+lbl&gt; &lt;dbl&gt;</span></span>
<span id="cb2-5"><a href="#cb2-5"></a><span class="co"># 1 10002 1 1 76.6</span></span>
<span id="cb2-6"><a href="#cb2-6"></a><span class="co"># 2 10004 0 1 59.1</span></span>
<span id="cb2-7"><a href="#cb2-7"></a><span class="co"># 3 10005 1 1 54.5</span></span>
<span id="cb2-8"><a href="#cb2-8"></a><span class="co"># 4 10006 1 1 54.1</span></span>
<span id="cb2-9"><a href="#cb2-9"></a><span class="co"># 5 10007 1 1 57.7</span></span>
<span id="cb2-10"><a href="#cb2-10"></a><span class="co"># 6 10008 1 1 62.8</span></span>
<span id="cb2-11"><a href="#cb2-11"></a><span class="co"># 7 10010 0 1 63.7</span></span>
<span id="cb2-12"><a href="#cb2-12"></a><span class="co"># 8 10011 1 1 73.1</span></span>
<span id="cb2-13"><a href="#cb2-13"></a><span class="co"># 9 10017 1 1 56.7</span></span>
<span id="cb2-14"><a href="#cb2-14"></a><span class="co"># 10 10018 0 1 66.6</span></span>
<span id="cb2-15"><a href="#cb2-15"></a><span class="co"># # … with 4,193 more rows</span></span>
<span id="cb2-16"><a href="#cb2-16"></a></span>
<span id="cb2-17"><a href="#cb2-17"></a><span class="kw">as_factor</span>(SPSS_data)</span>
<span id="cb2-18"><a href="#cb2-18"></a><span class="co"># # A tibble: 4,203 x 4</span></span>
<span id="cb2-19"><a href="#cb2-19"></a><span class="co"># v001 sex status statusage</span></span>
<span id="cb2-20"><a href="#cb2-20"></a><span class="co"># &lt;dbl&gt; &lt;fct&gt; &lt;fct&gt; &lt;dbl&gt;</span></span>
<span id="cb2-21"><a href="#cb2-21"></a><span class="co"># 1 10002 Male alive 76.6</span></span>
<span id="cb2-22"><a href="#cb2-22"></a><span class="co"># 2 10004 Female alive 59.1</span></span>
<span id="cb2-23"><a href="#cb2-23"></a><span class="co"># 3 10005 Male alive 54.5</span></span>
<span id="cb2-24"><a href="#cb2-24"></a><span class="co"># 4 10006 Male alive 54.1</span></span>
<span id="cb2-25"><a href="#cb2-25"></a><span class="co"># 5 10007 Male alive 57.7</span></span>
<span id="cb2-26"><a href="#cb2-26"></a><span class="co"># 6 10008 Male alive 62.8</span></span>
<span id="cb2-27"><a href="#cb2-27"></a><span class="co"># 7 10010 Female alive 63.7</span></span>
<span id="cb2-28"><a href="#cb2-28"></a><span class="co"># 8 10011 Male alive 73.1</span></span>
<span id="cb2-29"><a href="#cb2-29"></a><span class="co"># 9 10017 Male alive 56.7</span></span>
<span id="cb2-30"><a href="#cb2-30"></a><span class="co"># 10 10018 Female alive 66.6</span></span>
<span id="cb2-31"><a href="#cb2-31"></a><span class="co"># # … with 4,193 more rows</span></span></code></pre></div>
</div>
<div id="base-r" class="section level3">
<h3 class="hasAnchor">
<a href="#base-r" class="anchor"></a>Base R</h3>
<p>To import data from SPSS, SAS or Stata, you can use the <a href="https://haven.tidyverse.org/">great <code>haven</code> package</a> yourself:</p>
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" data-line-number="1"><span class="co"># download and install the latest version:</span></a>
<a class="sourceLine" id="cb3-2" data-line-number="2"><span class="kw"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span>(<span class="st">"haven"</span>)</a>
<a class="sourceLine" id="cb3-3" data-line-number="3"><span class="co"># load the package you just installed:</span></a>
<a class="sourceLine" id="cb3-4" data-line-number="4"><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span>(haven) </a></code></pre></div>
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb3-1"><a href="#cb3-1"></a><span class="co"># download and install the latest version:</span></span>
<span id="cb3-2"><a href="#cb3-2"></a><span class="kw"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span>(<span class="st">"haven"</span>)</span>
<span id="cb3-3"><a href="#cb3-3"></a><span class="co"># load the package you just installed:</span></span>
<span id="cb3-4"><a href="#cb3-4"></a><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span>(haven) </span></code></pre></div>
<p>You can now import files as follows:</p>
<div id="spss" class="section level4">
<h4 class="hasAnchor">
<a href="#spss" class="anchor"></a>SPSS</h4>
<p>To read files from SPSS into R:</p>
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" data-line-number="1"><span class="co"># read any SPSS file based on file extension (best way):</span></a>
<a class="sourceLine" id="cb4-2" data-line-number="2"><span class="kw"><a href="https://haven.tidyverse.org/reference/read_spss.html">read_spss</a></span>(<span class="dt">file =</span> <span class="st">"path/to/file"</span>)</a>
<a class="sourceLine" id="cb4-3" data-line-number="3"></a>
<a class="sourceLine" id="cb4-4" data-line-number="4"><span class="co"># read .sav or .zsav file:</span></a>
<a class="sourceLine" id="cb4-5" data-line-number="5"><span class="kw"><a href="https://haven.tidyverse.org/reference/read_spss.html">read_sav</a></span>(<span class="dt">file =</span> <span class="st">"path/to/file"</span>)</a>
<a class="sourceLine" id="cb4-6" data-line-number="6"></a>
<a class="sourceLine" id="cb4-7" data-line-number="7"><span class="co"># read .por file:</span></a>
<a class="sourceLine" id="cb4-8" data-line-number="8"><span class="kw"><a href="https://haven.tidyverse.org/reference/read_spss.html">read_por</a></span>(<span class="dt">file =</span> <span class="st">"path/to/file"</span>)</a></code></pre></div>
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb4-1"><a href="#cb4-1"></a><span class="co"># read any SPSS file based on file extension (best way):</span></span>
<span id="cb4-2"><a href="#cb4-2"></a><span class="kw"><a href="https://haven.tidyverse.org/reference/read_spss.html">read_spss</a></span>(<span class="dt">file =</span> <span class="st">"path/to/file"</span>)</span>
<span id="cb4-3"><a href="#cb4-3"></a></span>
<span id="cb4-4"><a href="#cb4-4"></a><span class="co"># read .sav or .zsav file:</span></span>
<span id="cb4-5"><a href="#cb4-5"></a><span class="kw"><a href="https://haven.tidyverse.org/reference/read_spss.html">read_sav</a></span>(<span class="dt">file =</span> <span class="st">"path/to/file"</span>)</span>
<span id="cb4-6"><a href="#cb4-6"></a></span>
<span id="cb4-7"><a href="#cb4-7"></a><span class="co"># read .por file:</span></span>
<span id="cb4-8"><a href="#cb4-8"></a><span class="kw"><a href="https://haven.tidyverse.org/reference/read_spss.html">read_por</a></span>(<span class="dt">file =</span> <span class="st">"path/to/file"</span>)</span></code></pre></div>
<p>Do not forget about <code><a href="https://haven.tidyverse.org/reference/as_factor.html">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="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" data-line-number="1"><span class="co"># save as .sav file:</span></a>
<a class="sourceLine" id="cb5-2" data-line-number="2"><span class="kw"><a href="https://haven.tidyverse.org/reference/read_spss.html">write_sav</a></span>(<span class="dt">data =</span> yourdata, <span class="dt">path =</span> <span class="st">"path/to/file"</span>)</a>
<a class="sourceLine" id="cb5-3" data-line-number="3"></a>
<a class="sourceLine" id="cb5-4" data-line-number="4"><span class="co"># save as compressed .zsav file:</span></a>
<a class="sourceLine" id="cb5-5" data-line-number="5"><span class="kw"><a href="https://haven.tidyverse.org/reference/read_spss.html">write_sav</a></span>(<span class="dt">data =</span> yourdata, <span class="dt">path =</span> <span class="st">"path/to/file"</span>, <span class="dt">compress =</span> <span class="ot">TRUE</span>)</a></code></pre></div>
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb5-1"><a href="#cb5-1"></a><span class="co"># save as .sav file:</span></span>
<span id="cb5-2"><a href="#cb5-2"></a><span class="kw"><a href="https://haven.tidyverse.org/reference/read_spss.html">write_sav</a></span>(<span class="dt">data =</span> yourdata, <span class="dt">path =</span> <span class="st">"path/to/file"</span>)</span>
<span id="cb5-3"><a href="#cb5-3"></a></span>
<span id="cb5-4"><a href="#cb5-4"></a><span class="co"># save as compressed .zsav file:</span></span>
<span id="cb5-5"><a href="#cb5-5"></a><span class="kw"><a href="https://haven.tidyverse.org/reference/read_spss.html">write_sav</a></span>(<span class="dt">data =</span> yourdata, <span class="dt">path =</span> <span class="st">"path/to/file"</span>, <span class="dt">compress =</span> <span class="ot">TRUE</span>)</span></code></pre></div>
</div>
<div id="sas" class="section level4">
<h4 class="hasAnchor">
<a href="#sas" class="anchor"></a>SAS</h4>
<p>To read files from SAS into R:</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="co"># read .sas7bdat + .sas7bcat files:</span></a>
<a class="sourceLine" id="cb6-2" data-line-number="2"><span class="kw"><a href="https://haven.tidyverse.org/reference/read_sas.html">read_sas</a></span>(<span class="dt">data_file =</span> <span class="st">"path/to/file"</span>, <span class="dt">catalog_file =</span> <span class="ot">NULL</span>)</a>
<a class="sourceLine" id="cb6-3" data-line-number="3"></a>
<a class="sourceLine" id="cb6-4" data-line-number="4"><span class="co"># read SAS transport files (version 5 and version 8):</span></a>
<a class="sourceLine" id="cb6-5" data-line-number="5"><span class="kw"><a href="https://haven.tidyverse.org/reference/read_xpt.html">read_xpt</a></span>(<span class="dt">file =</span> <span class="st">"path/to/file"</span>)</a></code></pre></div>
<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb6-1"><a href="#cb6-1"></a><span class="co"># read .sas7bdat + .sas7bcat files:</span></span>
<span id="cb6-2"><a href="#cb6-2"></a><span class="kw"><a href="https://haven.tidyverse.org/reference/read_sas.html">read_sas</a></span>(<span class="dt">data_file =</span> <span class="st">"path/to/file"</span>, <span class="dt">catalog_file =</span> <span class="ot">NULL</span>)</span>
<span id="cb6-3"><a href="#cb6-3"></a></span>
<span id="cb6-4"><a href="#cb6-4"></a><span class="co"># read SAS transport files (version 5 and version 8):</span></span>
<span id="cb6-5"><a href="#cb6-5"></a><span class="kw"><a href="https://haven.tidyverse.org/reference/read_xpt.html">read_xpt</a></span>(<span class="dt">file =</span> <span class="st">"path/to/file"</span>)</span></code></pre></div>
<p>To export your R objects to the SAS file format:</p>
<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" data-line-number="1"><span class="co"># save as regular SAS file:</span></a>
<a class="sourceLine" id="cb7-2" data-line-number="2"><span class="kw"><a href="https://haven.tidyverse.org/reference/read_sas.html">write_sas</a></span>(<span class="dt">data =</span> yourdata, <span class="dt">path =</span> <span class="st">"path/to/file"</span>)</a>
<a class="sourceLine" id="cb7-3" data-line-number="3"></a>
<a class="sourceLine" id="cb7-4" data-line-number="4"><span class="co"># the SAS transport format is an open format </span></a>
<a class="sourceLine" id="cb7-5" data-line-number="5"><span class="co"># (required for submission of the data to the FDA)</span></a>
<a class="sourceLine" id="cb7-6" data-line-number="6"><span class="kw"><a href="https://haven.tidyverse.org/reference/read_xpt.html">write_xpt</a></span>(<span class="dt">data =</span> yourdata, <span class="dt">path =</span> <span class="st">"path/to/file"</span>, <span class="dt">version =</span> <span class="dv">8</span>)</a></code></pre></div>
<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb7-1"><a href="#cb7-1"></a><span class="co"># save as regular SAS file:</span></span>
<span id="cb7-2"><a href="#cb7-2"></a><span class="kw"><a href="https://haven.tidyverse.org/reference/read_sas.html">write_sas</a></span>(<span class="dt">data =</span> yourdata, <span class="dt">path =</span> <span class="st">"path/to/file"</span>)</span>
<span id="cb7-3"><a href="#cb7-3"></a></span>
<span id="cb7-4"><a href="#cb7-4"></a><span class="co"># the SAS transport format is an open format </span></span>
<span id="cb7-5"><a href="#cb7-5"></a><span class="co"># (required for submission of the data to the FDA)</span></span>
<span id="cb7-6"><a href="#cb7-6"></a><span class="kw"><a href="https://haven.tidyverse.org/reference/read_xpt.html">write_xpt</a></span>(<span class="dt">data =</span> yourdata, <span class="dt">path =</span> <span class="st">"path/to/file"</span>, <span class="dt">version =</span> <span class="dv">8</span>)</span></code></pre></div>
</div>
<div id="stata" class="section level4">
<h4 class="hasAnchor">
<a href="#stata" class="anchor"></a>Stata</h4>
<p>To read files from Stata into R:</p>
<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" data-line-number="1"><span class="co"># read .dta file:</span></a>
<a class="sourceLine" id="cb8-2" data-line-number="2"><span class="kw"><a href="https://haven.tidyverse.org/reference/read_dta.html">read_stata</a></span>(<span class="dt">file =</span> <span class="st">"/path/to/file"</span>)</a>
<a class="sourceLine" id="cb8-3" data-line-number="3"></a>
<a class="sourceLine" id="cb8-4" data-line-number="4"><span class="co"># works exactly the same:</span></a>
<a class="sourceLine" id="cb8-5" data-line-number="5"><span class="kw"><a href="https://haven.tidyverse.org/reference/read_dta.html">read_dta</a></span>(<span class="dt">file =</span> <span class="st">"/path/to/file"</span>)</a></code></pre></div>
<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb8-1"><a href="#cb8-1"></a><span class="co"># read .dta file:</span></span>
<span id="cb8-2"><a href="#cb8-2"></a><span class="kw"><a href="https://haven.tidyverse.org/reference/read_dta.html">read_stata</a></span>(<span class="dt">file =</span> <span class="st">"/path/to/file"</span>)</span>
<span id="cb8-3"><a href="#cb8-3"></a></span>
<span id="cb8-4"><a href="#cb8-4"></a><span class="co"># works exactly the same:</span></span>
<span id="cb8-5"><a href="#cb8-5"></a><span class="kw"><a href="https://haven.tidyverse.org/reference/read_dta.html">read_dta</a></span>(<span class="dt">file =</span> <span class="st">"/path/to/file"</span>)</span></code></pre></div>
<p>To export your R objects to the Stata file format:</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="co"># save as .dta file, Stata version 14:</span></a>
<a class="sourceLine" id="cb9-2" data-line-number="2"><span class="co"># (supports Stata v8 until v15 at the time of writing)</span></a>
<a class="sourceLine" id="cb9-3" data-line-number="3"><span class="kw"><a href="https://haven.tidyverse.org/reference/read_dta.html">write_dta</a></span>(<span class="dt">data =</span> yourdata, <span class="dt">path =</span> <span class="st">"/path/to/file"</span>, <span class="dt">version =</span> <span class="dv">14</span>)</a></code></pre></div>
<div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb9-1"><a href="#cb9-1"></a><span class="co"># save as .dta file, Stata version 14:</span></span>
<span id="cb9-2"><a href="#cb9-2"></a><span class="co"># (supports Stata v8 until v15 at the time of writing)</span></span>
<span id="cb9-3"><a href="#cb9-3"></a><span class="kw"><a href="https://haven.tidyverse.org/reference/read_dta.html">write_dta</a></span>(<span class="dt">data =</span> yourdata, <span class="dt">path =</span> <span class="st">"/path/to/file"</span>, <span class="dt">version =</span> <span class="dv">14</span>)</span></code></pre></div>
</div>
</div>
</div>
@ -414,20 +406,7 @@
</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>
</body>
</html>