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<img src="../logo.png" class="logo" alt=""><h1>Database-creation</h1>
<small class="dont-index">Source: <a href="https://github.com/agdamsbo/REDCapCAST/blob/v24.12.1/vignettes/Database-creation.Rmd" class="external-link"><code>vignettes/Database-creation.Rmd</code></a></small>
<div class="d-none name"><code>Database-creation.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://github.com/agdamsbo/REDCapCAST" class="external-link">REDCapCAST</a></span><span class="op">)</span></span></code></pre></div>
<div class="section level2">
<h2 id="two-different-ways-to-create-a-data-base">Two different ways to create a data base<a class="anchor" aria-label="anchor" href="#two-different-ways-to-create-a-data-base"></a>
</h2>
<p><code>REDCapCAST</code> provides two approaches to creating a data
dictionary aimed at helping out in two different cases:</p>
<ol style="list-style-type: decimal">
<li><p>Easily create a REDCap data base from an existing data
set.</p></li>
<li><p>Create a table in Word describing a variables in a data base and
use this to create a data base.</p></li>
</ol>
<p>In the following I will try to come with a few suggestions on how to
use these approaches.</p>
<div class="section level3">
<h3 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>
</h3>
<p>The first iteration of a dataset to data dictionary function is the
<code><a href="../reference/ds2dd.html">ds2dd()</a></code>, which creates a very basic data dictionary with
all variables stored as text. This is sufficient for just storing old
datasets/spreadsheets securely in REDCap.</p>
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">d1</span> <span class="op">&lt;-</span> <span class="va">mtcars</span> <span class="op">|&gt;</span></span>
<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">|&gt;</span></span>
<span> <span class="fu"><a href="../reference/ds2dd.html">ds2dd</a></span><span class="op">(</span><span class="op">)</span> </span>
<span></span>
<span><span class="va">d1</span> <span class="op">|&gt;</span></span>
<span> <span class="fu">gt</span><span class="fu">::</span><span class="fu"><a href="https://gt.rstudio.com/reference/gt.html" class="external-link">gt</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
<p>The more advanced <code><a href="../reference/ds2dd_detailed.html">ds2dd_detailed()</a></code> is a natural
development. It will try to apply the most common data classes for data
validation and will assume that the first column is the id number. It
outputs a list with the dataset with modified variable names to comply
with REDCap naming conventions and a data dictionary.</p>
<p>The dataset should be correctly formatted for the data dictionary to
preserve as much information as possible.</p>
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">d2</span> <span class="op">&lt;-</span> <span class="fu">REDCapCAST</span><span class="fu">::</span><span class="va"><a href="../reference/redcapcast_data.html">redcapcast_data</a></span> <span class="op">|&gt;</span> </span>
<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>
<span> region<span class="op">=</span><span class="fu"><a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a></span><span class="op">(</span><span class="va">region</span><span class="op">)</span><span class="op">)</span> <span class="op">|&gt;</span></span>
<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">|&gt;</span></span>
<span> <span class="op">(</span>\<span class="op">(</span><span class="va">.x</span><span class="op">)</span><span class="op">{</span></span>
<span> <span class="va">.x</span><span class="op">[</span><span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/grep.html" class="external-link">grepl</a></span><span class="op">(</span><span class="st">"_complete$"</span>,<span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">.x</span><span class="op">)</span><span class="op">)</span><span class="op">]</span></span>
<span> <span class="op">}</span><span class="op">)</span><span class="op">(</span><span class="op">)</span> <span class="op">|&gt;</span> </span>
<span> <span class="op">(</span>\<span class="op">(</span><span class="va">.x</span><span class="op">)</span><span class="op">{</span></span>
<span> <span class="va">.x</span><span class="op">[</span><span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/grep.html" class="external-link">grepl</a></span><span class="op">(</span><span class="st">"^redcap"</span>,<span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">.x</span><span class="op">)</span><span class="op">)</span><span class="op">]</span></span>
<span> <span class="op">}</span><span class="op">)</span><span class="op">(</span><span class="op">)</span> <span class="op">|&gt;</span> </span>
<span> <span class="fu"><a href="../reference/ds2dd_detailed.html">ds2dd_detailed</a></span><span class="op">(</span><span class="op">)</span> <span class="op">|&gt;</span> </span>
<span> <span class="fu">purrr</span><span class="fu">::</span><span class="fu"><a href="https://purrr.tidyverse.org/reference/pluck.html" class="external-link">pluck</a></span><span class="op">(</span><span class="st">"meta"</span><span class="op">)</span> </span>
<span></span>
<span><span class="va">d2</span> <span class="op">|&gt;</span> </span>
<span> <span class="fu">gt</span><span class="fu">::</span><span class="fu"><a href="https://gt.rstudio.com/reference/gt.html" class="external-link">gt</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
<p>Additional specifications to the DataDictionary can be made manually,
or it can be uploaded and modified manually in the graphical user
interface on the REDCap server.</p>
</div>
<div class="section level3">
<h3 id="data-base-from-table">Data base from table<a class="anchor" aria-label="anchor" href="#data-base-from-table"></a>
</h3>
<p>…instructions and examples are coming…</p>
</div>
<div class="section level3">
<h3 id="meta-data-and-data-upload">Meta data and data upload<a class="anchor" aria-label="anchor" href="#meta-data-and-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">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>
</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"><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>
<span> <span class="va">dd_ls</span><span class="op">$</span><span class="va">meta</span>,</span>
<span> redcap_uri <span class="op">=</span> <span class="fu">keyring</span><span class="fu">::</span><span class="fu"><a href="https://keyring.r-lib.org/reference/key_get.html" class="external-link">key_get</a></span><span class="op">(</span><span class="st">"DB_URI"</span><span class="op">)</span>,</span>
<span> token <span class="op">=</span> <span class="fu">keyring</span><span class="fu">::</span><span class="fu"><a href="https://keyring.r-lib.org/reference/key_get.html" class="external-link">key_get</a></span><span class="op">(</span><span class="st">"DB_TOKEN"</span><span class="op">)</span></span>
<span><span class="op">)</span></span></code></pre></div>
<p>In the <a href="https://agdamsbo.github.io/redcap-r-handbook/" class="external-link">“REDCap R
Handbook”</a> more is written on interfacing with REDCap in R using the
<code><a href="https://keyring.r-lib.org/" class="external-link">library(keyring)</a></code>to store credentials in <a href="https://agdamsbo.github.io/redcap-r-handbook/doc/access.html#sec-getting-access" class="external-link">chapter
1.1</a>.</p>
</div>
</div>
<div class="section level3">
<h3 id="step-4---data-upload">Step 4 - Data upload<a class="anchor" aria-label="anchor" href="#step-4---data-upload"></a>
</h3>
<p>The same two options are available for data upload as meta data
upload: manual or through <code>REDCapR</code>.</p>
<p>Only the latter is shown here.</p>
<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu">REDCapR</span><span class="fu">::</span><span class="fu"><a href="https://ouhscbbmc.github.io/REDCapR/reference/redcap_write.html" class="external-link">redcap_write</a></span><span class="op">(</span></span>
<span> <span class="va">dd_ls</span><span class="op">$</span><span class="va">data</span>,</span>
<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>
<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>
<span><span class="op">)</span></span></code></pre></div>
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