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<img src="../logo.png" class="logo" alt=""><h1>Database-creation</h1>
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<small class="dont-index">Source: <a href="https://github.com/agdamsbo/REDCapCAST/blob/HEAD/vignettes/Database-creation.Rmd" class="external-link"><code>vignettes/Database-creation.Rmd</code></a></small>
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<div class="d-none name"><code>Database-creation.Rmd</code></div>
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</div>
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<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
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<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://github.com/agdamsbo/REDCapCAST" class="external-link">REDCapCAST</a></span><span class="op">)</span></span></code></pre></div>
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<div class="section level2">
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<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>
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</h2>
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<p>THe first iteration of a dataset to data dictionary function is the
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<code><a href="../reference/ds2dd.html">ds2dd()</a></code>, which creates a very basic data dictionary with
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all variables stored as text. This is sufficient for just storing old
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datasets/spreadsheets securely in REDCap.</p>
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<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
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<code class="sourceCode R"><span><span class="va">mtcars</span> <span class="op">|></span></span>
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<span> <span class="fu">dplyr</span><span class="fu">::</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>record_id <span class="op">=</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">dplyr</span><span class="fu">::</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/context.html" class="external-link">n</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="op">)</span> <span class="op">|></span></span>
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<span> <span class="fu"><a href="../reference/ds2dd.html">ds2dd</a></span><span class="op">(</span><span class="op">)</span> <span class="op">|></span></span>
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<span> <span class="fu"><a href="https://rdrr.io/r/utils/str.html" class="external-link">str</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
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<p>The more advanced <code><a href="../reference/ds2dd_detailed.html">ds2dd_detailed()</a></code> is a natural
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development. It will try to apply the most common data classes for data
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validation and will assume that the first column is the id number. It
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outputs a list with the dataset with modified variable names to comply
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with REDCap naming conventions and a data dictionary.</p>
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<p>The dataset should be correctly formatted for the data dictionary to
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preserve as much information as possible.</p>
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<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
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<code class="sourceCode R"><span><span class="va">dd_ls</span> <span class="op"><-</span> <span class="va">mtcars</span> <span class="op">|></span></span>
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<span> <span class="fu">dplyr</span><span class="fu">::</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>record_id <span class="op">=</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">dplyr</span><span class="fu">::</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/context.html" class="external-link">n</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="op">)</span> <span class="op">|></span></span>
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<span> <span class="fu">dplyr</span><span class="fu">::</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">record_id</span>, <span class="fu">dplyr</span><span class="fu">::</span><span class="fu"><a href="https://tidyselect.r-lib.org/reference/everything.html" class="external-link">everything</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="op">|></span></span>
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<span> <span class="fu"><a href="../reference/ds2dd_detailed.html">ds2dd_detailed</a></span><span class="op">(</span><span class="op">)</span></span>
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<span><span class="va">dd_ls</span> <span class="op">|></span> </span>
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<span> <span class="fu"><a href="https://rdrr.io/r/utils/str.html" class="external-link">str</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
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<p>Additional specifications to the DataDictionary can be made manually,
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or it can be uploaded and modified manually in the graphical user
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interface on the web page.</p>
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<div class="section level3">
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<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>
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</h3>
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<p>Now the DataDictionary can be exported as a spreadsheet and uploaded
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or it can be uploaded using the <code>REDCapR</code> package (only
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projects with “Development” status).</p>
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<p>Use one of the two approaches below:</p>
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<div class="section level4">
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<h4 id="manual-upload">Manual upload<a class="anchor" aria-label="anchor" href="#manual-upload"></a>
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</h4>
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<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
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<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">dd_ls</span><span class="op">$</span><span class="va">meta</span>, <span class="st">"datadictionary.csv"</span><span class="op">)</span></span></code></pre></div>
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</div>
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<div class="section level4">
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<h4 id="upload-with-redcapr">Upload with <code>REDCapR</code><a class="anchor" aria-label="anchor" href="#upload-with-redcapr"></a>
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</h4>
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<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
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<code class="sourceCode R"><span><span class="fu">REDCapR</span><span class="fu">::</span><span class="fu"><a href="https://ouhscbbmc.github.io/REDCapR/reference/redcap_metadata_write.html" class="external-link">redcap_metadata_write</a></span><span class="op">(</span></span>
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<span> <span class="va">dd_ls</span><span class="op">$</span><span class="va">meta</span>,</span>
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<span> redcap_uri <span class="op">=</span> <span class="fu">keyring</span><span class="fu">::</span><span class="fu"><a href="https://keyring.r-lib.org/reference/key_get.html" class="external-link">key_get</a></span><span class="op">(</span><span class="st">"DB_URI"</span><span class="op">)</span>,</span>
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<span> token <span class="op">=</span> <span class="fu">keyring</span><span class="fu">::</span><span class="fu"><a href="https://keyring.r-lib.org/reference/key_get.html" class="external-link">key_get</a></span><span class="op">(</span><span class="st">"DB_TOKEN"</span><span class="op">)</span></span>
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<span><span class="op">)</span></span></code></pre></div>
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<p>In the <a href="https://agdamsbo.github.io/redcap-r-handbook/" class="external-link">“REDCap R
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Handbook”</a> more is written on interfacing with REDCap in R using the
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<code><a href="https://keyring.r-lib.org/" class="external-link">library(keyring)</a></code>to store credentials in <a href="https://agdamsbo.github.io/redcap-r-handbook/doc/access.html#sec-getting-access" class="external-link">chapter
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1.1</a>.</p>
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</div>
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</div>
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<div class="section level3">
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<h3 id="step-4---data-upload">Step 4 - Data upload<a class="anchor" aria-label="anchor" href="#step-4---data-upload"></a>
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</h3>
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<p>The same two options are available for data upload as meta data
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upload: manual or through <code>REDCapR</code>.</p>
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<p>Only the latter is shown here.</p>
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<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
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<code class="sourceCode R"><span><span class="fu">REDCapR</span><span class="fu">::</span><span class="fu"><a href="https://ouhscbbmc.github.io/REDCapR/reference/redcap_write.html" class="external-link">redcap_write</a></span><span class="op">(</span></span>
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<span> <span class="va">dd_ls</span><span class="op">$</span><span class="va">data</span>,</span>
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<span> redcap_uri <span class="op">=</span> <span class="fu">keyring</span><span class="fu">::</span><span class="fu"><a href="https://keyring.r-lib.org/reference/key_get.html" class="external-link">key_get</a></span><span class="op">(</span><span class="st">"DB_URI"</span><span class="op">)</span>,</span>
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<span> token <span class="op">=</span> <span class="fu">keyring</span><span class="fu">::</span><span class="fu"><a href="https://keyring.r-lib.org/reference/key_get.html" class="external-link">key_get</a></span><span class="op">(</span><span class="st">"DB_TOKEN"</span><span class="op">)</span></span>
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<span><span class="op">)</span></span></code></pre></div>
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