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dr. M.S. (Matthijs) Berends
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</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">1.3.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
</span>
</div>
@ -186,7 +186,7 @@
<h1 data-toc-skip>How to import data from SPSS / SAS / Stata</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">30 July 2020</h4>
<h4 class="date">10 August 2020</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/SPSS.Rmd"><code>vignettes/SPSS.Rmd</code></a></small>
<div class="hidden name"><code>SPSS.Rmd</code></div>
@ -240,7 +240,8 @@
</li>
</ul>
<p>To demonstrate the first point:</p>
<div class="sourceCode" id="cb1"><html><body><pre class="r"><span class="co"># not all values are valid MIC values:</span>
<div class="sourceCode" id="cb1"><pre class="downlit">
<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="fl">0.125</span>)
<span class="co"># Class &lt;mic&gt;</span>
<span class="co"># [1] 0.125</span>
@ -253,13 +254,13 @@
<span class="co"># [1] "Gram-negative"</span>
<span class="co"># Klebsiella is intrinsic resistant to amoxicllin, according to EUCAST:</span>
<span class="no">klebsiella_test</span> <span class="kw">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span>(<span class="kw">mo</span> <span class="kw">=</span> <span class="st">"klebsiella"</span>,
<span class="kw">amox</span> <span class="kw">=</span> <span class="st">"S"</span>,
<span class="kw">stringsAsFactors</span> <span class="kw">=</span> <span class="fl">FALSE</span>)
<span class="no">klebsiella_test</span> <span class="co"># (our original data)</span>
<span class="kw">klebsiella_test</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span>(mo = <span class="st">"klebsiella"</span>,
amox = <span class="st">"S"</span>,
stringsAsFactors = <span class="fl">FALSE</span>)
<span class="kw">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="no">klebsiella_test</span>, <span class="kw">info</span> <span class="kw">=</span> <span class="fl">FALSE</span>) <span class="co"># (the edited data by EUCAST rules)</span>
<span class="fu"><a href="../reference/eucast_rules.html">eucast_rules</a></span>(<span class="kw">klebsiella_test</span>, info = <span class="fl">FALSE</span>) <span class="co"># (the edited data by EUCAST rules)</span>
<span class="co"># mo amox</span>
<span class="co"># 1 klebsiella R</span>
@ -271,7 +272,8 @@
<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="st">"floxapen"</span>)
<span class="co"># [1] "J01CF05"</span></pre></body></html></div>
<span class="co"># [1] "J01CF05"</span>
</pre></div>
</div>
<div id="import-data-from-spsssasstata" class="section level2">
<h2 class="hasAnchor">
@ -287,7 +289,8 @@
<p><img src="https://github.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"><html><body><pre class="r"><span class="no">SPSS_data</span>
<div class="sourceCode" id="cb2"><pre class="downlit">
<span class="kw">SPSS_data</span>
<span class="co"># # A tibble: 4,203 x 4</span>
<span class="co"># v001 sex status statusage</span>
<span class="co"># &lt;dbl&gt; &lt;dbl+lbl&gt; &lt;dbl+lbl&gt; &lt;dbl&gt;</span>
@ -303,7 +306,7 @@
<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="no">SPSS_data</span>)
<span class="fu">as_factor</span>(<span class="kw">SPSS_data</span>)
<span class="co"># # A tibble: 4,203 x 4</span>
<span class="co"># v001 sex status statusage</span>
<span class="co"># &lt;dbl&gt; &lt;fct&gt; &lt;fct&gt; &lt;dbl&gt;</span>
@ -317,67 +320,82 @@
<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></pre></body></html></div>
<span class="co"># # … with 4,193 more rows</span>
</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"><html><body><pre class="r"><span class="co"># download and install the latest version:</span>
<div class="sourceCode" id="cb3"><pre class="downlit">
<span class="co"># download and install the latest version:</span>
<span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span>(<span class="st">"haven"</span>)
<span class="co"># load the package you just installed:</span>
<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="no">haven</span>)</pre></body></html></div>
<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="kw"><a href="http://haven.tidyverse.org">haven</a></span>)
</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"><html><body><pre class="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">read_spss</a></span>(<span class="kw">file</span> <span class="kw">=</span> <span class="st">"path/to/file"</span>)
<div class="sourceCode" id="cb4"><pre class="downlit">
<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">read_spss</a></span>(file = <span class="st">"path/to/file"</span>)
<span class="co"># read .sav or .zsav file:</span>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_spss.html">read_sav</a></span>(<span class="kw">file</span> <span class="kw">=</span> <span class="st">"path/to/file"</span>)
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_spss.html">read_sav</a></span>(file = <span class="st">"path/to/file"</span>)
<span class="co"># read .por file:</span>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_spss.html">read_por</a></span>(<span class="kw">file</span> <span class="kw">=</span> <span class="st">"path/to/file"</span>)</pre></body></html></div>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_spss.html">read_por</a></span>(file = <span class="st">"path/to/file"</span>)
</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"><html><body><pre class="r"><span class="co"># save as .sav file:</span>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_spss.html">write_sav</a></span>(<span class="kw">data</span> <span class="kw">=</span> <span class="no">yourdata</span>, <span class="kw">path</span> <span class="kw">=</span> <span class="st">"path/to/file"</span>)
<div class="sourceCode" id="cb5"><pre class="downlit">
<span class="co"># save as .sav file:</span>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_spss.html">write_sav</a></span>(data = <span class="kw">yourdata</span>, path = <span class="st">"path/to/file"</span>)
<span class="co"># save as compressed .zsav file:</span>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_spss.html">write_sav</a></span>(<span class="kw">data</span> <span class="kw">=</span> <span class="no">yourdata</span>, <span class="kw">path</span> <span class="kw">=</span> <span class="st">"path/to/file"</span>, <span class="kw">compress</span> <span class="kw">=</span> <span class="fl">TRUE</span>)</pre></body></html></div>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_spss.html">write_sav</a></span>(data = <span class="kw">yourdata</span>, path = <span class="st">"path/to/file"</span>, compress = <span class="fl">TRUE</span>)
</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"><html><body><pre class="r"><span class="co"># read .sas7bdat + .sas7bcat files:</span>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_sas.html">read_sas</a></span>(<span class="kw">data_file</span> <span class="kw">=</span> <span class="st">"path/to/file"</span>, <span class="kw">catalog_file</span> <span class="kw">=</span> <span class="kw">NULL</span>)
<div class="sourceCode" id="cb6"><pre class="downlit">
<span class="co"># read .sas7bdat + .sas7bcat files:</span>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_sas.html">read_sas</a></span>(data_file = <span class="st">"path/to/file"</span>, catalog_file = <span class="kw">NULL</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">read_xpt</a></span>(<span class="kw">file</span> <span class="kw">=</span> <span class="st">"path/to/file"</span>)</pre></body></html></div>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_xpt.html">read_xpt</a></span>(file = <span class="st">"path/to/file"</span>)
</pre></div>
<p>To export your R objects to the SAS file format:</p>
<div class="sourceCode" id="cb7"><html><body><pre class="r"><span class="co"># save as regular SAS file:</span>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_sas.html">write_sas</a></span>(<span class="kw">data</span> <span class="kw">=</span> <span class="no">yourdata</span>, <span class="kw">path</span> <span class="kw">=</span> <span class="st">"path/to/file"</span>)
<div class="sourceCode" id="cb7"><pre class="downlit">
<span class="co"># save as regular SAS file:</span>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_sas.html">write_sas</a></span>(data = <span class="kw">yourdata</span>, path = <span class="st">"path/to/file"</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">write_xpt</a></span>(<span class="kw">data</span> <span class="kw">=</span> <span class="no">yourdata</span>, <span class="kw">path</span> <span class="kw">=</span> <span class="st">"path/to/file"</span>, <span class="kw">version</span> <span class="kw">=</span> <span class="fl">8</span>)</pre></body></html></div>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_xpt.html">write_xpt</a></span>(data = <span class="kw">yourdata</span>, path = <span class="st">"path/to/file"</span>, version = <span class="fl">8</span>)
</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"><html><body><pre class="r"><span class="co"># read .dta file:</span>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_dta.html">read_stata</a></span>(<span class="kw">file</span> <span class="kw">=</span> <span class="st">"/path/to/file"</span>)
<div class="sourceCode" id="cb8"><pre class="downlit">
<span class="co"># read .dta file:</span>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_dta.html">read_stata</a></span>(file = <span class="st">"/path/to/file"</span>)
<span class="co"># works exactly the same:</span>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_dta.html">read_dta</a></span>(<span class="kw">file</span> <span class="kw">=</span> <span class="st">"/path/to/file"</span>)</pre></body></html></div>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_dta.html">read_dta</a></span>(file = <span class="st">"/path/to/file"</span>)
</pre></div>
<p>To export your R objects to the Stata file format:</p>
<div class="sourceCode" id="cb9"><html><body><pre class="r"><span class="co"># save as .dta file, Stata version 14:</span>
<div class="sourceCode" id="cb9"><pre class="downlit">
<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">write_dta</a></span>(<span class="kw">data</span> <span class="kw">=</span> <span class="no">yourdata</span>, <span class="kw">path</span> <span class="kw">=</span> <span class="st">"/path/to/file"</span>, <span class="kw">version</span> <span class="kw">=</span> <span class="fl">14</span>)</pre></body></html></div>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_dta.html">write_dta</a></span>(data = <span class="kw">yourdata</span>, path = <span class="st">"/path/to/file"</span>, version = <span class="fl">14</span>)
</pre></div>
</div>
</div>
</div>
@ -398,7 +416,7 @@
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