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<main id="main" class="col-md-9"><div class="page-header">
<img src="../logo.png" class="logo" alt=""><h1>ds2dd</h1>
<h4 data-toc-skip class="date">2023-09-07</h4>
<small class="dont-index">Source: <a href="https://github.com/agdamsbo/stRoke/blob/HEAD/vignettes/ds2dd.Rmd" class="external-link"><code>vignettes/ds2dd.Rmd</code></a></small>
<div class="d-none name"><code>ds2dd.Rmd</code></div>
</div>
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
<code class="sourceCode R"><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://agdamsbo.github.io/stRoke/">stRoke</a></span><span class="op">)</span></span></code></pre></div>
<div class="section level2">
<h2 id="easy-data-set-to-data-base-workflow">Easy data set to data base workflow<a class="anchor" aria-label="anchor" href="#easy-data-set-to-data-base-workflow"></a>
</h2>
<p>This function can be used as a simple tool for creating at data base
metadata file for REDCap (called a DataDictionary) based on a given data
set file.</p>
<div class="section level3">
<h3 id="step-1---load-your-data-set">Step 1 - Load your data set<a class="anchor" aria-label="anchor" href="#step-1---load-your-data-set"></a>
</h3>
<p>Here we’ll use the sample TALOS dataset included with the
package.</p>
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="st">"talos"</span><span class="op">)</span></span>
<span><span class="va">ds</span> <span class="op">&lt;-</span> <span class="va">talos</span></span>
<span><span class="co"># As the data set lacks an ID column, one is added</span></span>
<span><span class="va">ds</span><span class="op">$</span><span class="va">id</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq_len</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/nrow.html" class="external-link">nrow</a></span><span class="op">(</span><span class="va">ds</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
</div>
<div class="section level3">
<h3 id="step-2---create-the-datadictionary">Step 2 - Create the DataDictionary<a class="anchor" aria-label="anchor" href="#step-2---create-the-datadictionary"></a>
</h3>
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">datadictionary</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/ds2dd.html">ds2dd</a></span><span class="op">(</span><span class="va">ds</span>,record.id <span class="op">=</span> <span class="st">"id"</span>,include.column.names <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div>
<p>Now additional specifications to the DataDictionary can be made
manually, or it can be uploaded and modified manually in the graphical
user interface on the web page.</p>
<p>The function will transform column names to lower case and substitute
spaces for underscores. The output is a list with the DataDictionary and
a vector of new column names for the dataset to fit the meta data.</p>
</div>
<div class="section level3">
<h3 id="step-3---meta-data-upload">Step 3 - Meta data upload<a class="anchor" aria-label="anchor" href="#step-3---meta-data-upload"></a>
</h3>
<p>Now the DataDictionary can be exported as a spreadsheet and uploaded
or it can be uploaded using the <code>REDCapR</code> package (only
projects with “Development” status).</p>
<p>Use one of the two approaches below:</p>
<div class="section level4">
<h4 id="manual-upload">Manual upload<a class="anchor" aria-label="anchor" href="#manual-upload"></a>
</h4>
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/write.table.html" class="external-link">write.csv</a></span><span class="op">(</span><span class="va">datadictionary</span><span class="op">$</span><span class="va">DataDictionary</span>,<span class="st">"datadictionary.csv"</span><span class="op">)</span></span></code></pre></div>
</div>
<div class="section level4">
<h4 id="upload-with-redcapr">Upload with <code>REDCapR</code><a class="anchor" aria-label="anchor" href="#upload-with-redcapr"></a>
</h4>
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu">REDCapR</span><span class="fu">::</span><span class="fu">redcap_metadata_write</span><span class="op">(</span></span>
<span> <span class="va">datadictionary</span><span class="op">$</span><span class="va">DataDictionary</span>,</span>
<span> redcap_uri <span class="op">=</span> <span class="fu">keyring</span><span class="fu">::</span><span class="fu">key_get</span><span class="op">(</span><span class="st">"DB_URI"</span><span class="op">)</span>,</span>
<span> token <span class="op">=</span> <span class="fu">keyring</span><span class="fu">::</span><span class="fu">key_get</span><span class="op">(</span><span class="st">"DB_TOKEN"</span><span class="op">)</span></span>
<span><span class="op">)</span></span></code></pre></div>
<p>In the <a href="https://agdamsbo.github.io/redcap-r-handbook/" class="external-link">“REDCap R
Handbook”</a> more is written on interfacing with REDCap in R using the
<code><a href="https://r-lib.github.io/keyring/index.html" class="external-link">library(keyring)</a></code>to store credentials in <a href="https://agdamsbo.github.io/redcap-r-handbook/access.html#sec-getting-access" class="external-link">chapter
1.1</a>.</p>
</div>
</div>
<div class="section level3">
<h3 id="step-4---data-upload">Step 4 - Data upload<a class="anchor" aria-label="anchor" href="#step-4---data-upload"></a>
</h3>
<p>The same two options are available for data upload as meta data
upload: manual or through <code>REDCapR</code>.</p>
<p>Only the latter is shown here.</p>
<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># new column names are applied</span></span>
<span><span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">colnames</a></span><span class="op">(</span><span class="va">ds</span><span class="op">)</span> <span class="op">&lt;-</span> <span class="va">datadictionary</span><span class="op">$</span><span class="va">`Column names`</span></span>
<span></span>
<span><span class="fu">REDCapR</span><span class="fu">::</span><span class="fu">redcap_write</span><span class="op">(</span></span>
<span> <span class="va">ds</span>,</span>
<span> redcap_uri <span class="op">=</span> <span class="fu">keyring</span><span class="fu">::</span><span class="fu">key_get</span><span class="op">(</span><span class="st">"DB_URI"</span><span class="op">)</span>,</span>
<span> token <span class="op">=</span> <span class="fu">keyring</span><span class="fu">::</span><span class="fu">key_get</span><span class="op">(</span><span class="st">"DB_TOKEN"</span><span class="op">)</span></span>
<span><span class="op">)</span></span></code></pre></div>
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