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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/HEAD/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="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>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">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 class="op">|&gt;</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>
<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">dd_ls</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">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="fu"><a href="../reference/ds2dd_detailed.html">ds2dd_detailed</a></span><span class="op">(</span><span class="op">)</span></span>
<span><span class="va">dd_ls</span> <span class="op">|&gt;</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>
<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 web page.</p>
<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">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/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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@ -48,7 +48,9 @@
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<div class="dropdown-menu" aria-labelledby="dropdown-articles"> <div class="dropdown-menu" aria-labelledby="dropdown-articles">
<a class="dropdown-item" href="../articles/Database-creation.html">Database-creation</a>
<a class="dropdown-item" href="../articles/Introduction.html">Introduction</a> <a class="dropdown-item" href="../articles/Introduction.html">Introduction</a>
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@ -98,23 +100,23 @@ demonstration of the functions.</p>
</h2> </h2>
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r"> <div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">redcapcast_data</span> <span class="op">|&gt;</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> <code class="sourceCode R"><span><span class="va">redcapcast_data</span> <span class="op">|&gt;</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>
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text-align: center; text-align: center;
border-bottom-color: #FFFFFF; border-bottom-color: #FFFFFF;
@ -181,13 +183,13 @@ demonstration of the functions.</p>
border-right-color: #D3D3D3; border-right-color: #D3D3D3;
} }
#fypiqpxsxm .gt_bottom_border { #tapeacohhi .gt_bottom_border {
border-bottom-style: solid; border-bottom-style: solid;
border-bottom-width: 2px; border-bottom-width: 2px;
border-bottom-color: #D3D3D3; border-bottom-color: #D3D3D3;
} }
#fypiqpxsxm .gt_col_headings { #tapeacohhi .gt_col_headings {
border-top-style: solid; border-top-style: solid;
border-top-width: 2px; border-top-width: 2px;
border-top-color: #D3D3D3; border-top-color: #D3D3D3;
@ -202,7 +204,7 @@ demonstration of the functions.</p>
border-right-color: #D3D3D3; border-right-color: #D3D3D3;
} }
#fypiqpxsxm .gt_col_heading { #tapeacohhi .gt_col_heading {
color: #333333; color: #333333;
background-color: #FFFFFF; background-color: #FFFFFF;
font-size: 100%; font-size: 100%;
@ -222,7 +224,7 @@ demonstration of the functions.</p>
overflow-x: hidden; overflow-x: hidden;
} }
#fypiqpxsxm .gt_column_spanner_outer { #tapeacohhi .gt_column_spanner_outer {
color: #333333; color: #333333;
background-color: #FFFFFF; background-color: #FFFFFF;
font-size: 100%; font-size: 100%;
@ -234,15 +236,15 @@ demonstration of the functions.</p>
padding-right: 4px; padding-right: 4px;
} }
#fypiqpxsxm .gt_column_spanner_outer:first-child { #tapeacohhi .gt_column_spanner_outer:first-child {
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#fypiqpxsxm .gt_column_spanner_outer:last-child { #tapeacohhi .gt_column_spanner_outer:last-child {
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border-bottom-style: solid; border-bottom-style: solid;
border-bottom-width: 2px; border-bottom-width: 2px;
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@ -254,11 +256,11 @@ demonstration of the functions.</p>
width: 100%; width: 100%;
} }
#fypiqpxsxm .gt_spanner_row { #tapeacohhi .gt_spanner_row {
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@ -284,7 +286,7 @@ demonstration of the functions.</p>
text-align: left; text-align: left;
} }
#fypiqpxsxm .gt_empty_group_heading { #tapeacohhi .gt_empty_group_heading {
padding: 0.5px; padding: 0.5px;
color: #333333; color: #333333;
background-color: #FFFFFF; background-color: #FFFFFF;
@ -299,15 +301,15 @@ demonstration of the functions.</p>
vertical-align: middle; vertical-align: middle;
} }
#fypiqpxsxm .gt_from_md > :first-child { #tapeacohhi .gt_from_md > :first-child {
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} }
#fypiqpxsxm .gt_from_md > :last-child { #tapeacohhi .gt_from_md > :last-child {
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@ -326,7 +328,7 @@ demonstration of the functions.</p>
overflow-x: hidden; overflow-x: hidden;
} }
#fypiqpxsxm .gt_stub { #tapeacohhi .gt_stub {
color: #333333; color: #333333;
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@ -339,7 +341,7 @@ demonstration of the functions.</p>
padding-right: 5px; padding-right: 5px;
} }
#fypiqpxsxm .gt_stub_row_group { #tapeacohhi .gt_stub_row_group {
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@ -353,15 +355,15 @@ demonstration of the functions.</p>
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@ -371,16 +373,16 @@ demonstration of the functions.</p>
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@ -390,7 +392,7 @@ demonstration of the functions.</p>
border-bottom-color: #D3D3D3; border-bottom-color: #D3D3D3;
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#fypiqpxsxm .gt_grand_summary_row { #tapeacohhi .gt_grand_summary_row {
color: #333333; color: #333333;
background-color: #FFFFFF; background-color: #FFFFFF;
text-transform: inherit; text-transform: inherit;
@ -400,7 +402,7 @@ demonstration of the functions.</p>
padding-right: 5px; padding-right: 5px;
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#fypiqpxsxm .gt_first_grand_summary_row { #tapeacohhi .gt_first_grand_summary_row {
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@ -410,7 +412,7 @@ demonstration of the functions.</p>
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#fypiqpxsxm .gt_last_grand_summary_row_top { #tapeacohhi .gt_last_grand_summary_row_top {
padding-top: 8px; padding-top: 8px;
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padding-left: 5px; padding-left: 5px;
@ -420,11 +422,11 @@ demonstration of the functions.</p>
border-bottom-color: #D3D3D3; border-bottom-color: #D3D3D3;
} }
#fypiqpxsxm .gt_striped { #tapeacohhi .gt_striped {
background-color: rgba(128, 128, 128, 0.05); background-color: rgba(128, 128, 128, 0.05);
} }
#fypiqpxsxm .gt_table_body { #tapeacohhi .gt_table_body {
border-top-style: solid; border-top-style: solid;
border-top-width: 2px; border-top-width: 2px;
border-top-color: #D3D3D3; border-top-color: #D3D3D3;
@ -433,7 +435,7 @@ demonstration of the functions.</p>
border-bottom-color: #D3D3D3; border-bottom-color: #D3D3D3;
} }
#fypiqpxsxm .gt_footnotes { #tapeacohhi .gt_footnotes {
color: #333333; color: #333333;
background-color: #FFFFFF; background-color: #FFFFFF;
border-bottom-style: none; border-bottom-style: none;
@ -447,7 +449,7 @@ demonstration of the functions.</p>
border-right-color: #D3D3D3; border-right-color: #D3D3D3;
} }
#fypiqpxsxm .gt_footnote { #tapeacohhi .gt_footnote {
margin: 0px; margin: 0px;
font-size: 90%; font-size: 90%;
padding-top: 4px; padding-top: 4px;
@ -456,7 +458,7 @@ demonstration of the functions.</p>
padding-right: 5px; padding-right: 5px;
} }
#fypiqpxsxm .gt_sourcenotes { #tapeacohhi .gt_sourcenotes {
color: #333333; color: #333333;
background-color: #FFFFFF; background-color: #FFFFFF;
border-bottom-style: none; border-bottom-style: none;
@ -470,7 +472,7 @@ demonstration of the functions.</p>
border-right-color: #D3D3D3; border-right-color: #D3D3D3;
} }
#fypiqpxsxm .gt_sourcenote { #tapeacohhi .gt_sourcenote {
font-size: 90%; font-size: 90%;
padding-top: 4px; padding-top: 4px;
padding-bottom: 4px; padding-bottom: 4px;
@ -478,63 +480,63 @@ demonstration of the functions.</p>
padding-right: 5px; padding-right: 5px;
} }
#fypiqpxsxm .gt_left { #tapeacohhi .gt_left {
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#fypiqpxsxm .gt_center { #tapeacohhi .gt_center {
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#fypiqpxsxm .gt_super { #tapeacohhi .gt_super {
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#fypiqpxsxm .gt_footnote_marks { #tapeacohhi .gt_footnote_marks {
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position: initial; position: initial;
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#fypiqpxsxm .gt_asterisk { #tapeacohhi .gt_asterisk {
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#fypiqpxsxm .gt_indent_3 { #tapeacohhi .gt_indent_3 {
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} }
#fypiqpxsxm .gt_indent_4 { #tapeacohhi .gt_indent_4 {
text-indent: 20px; text-indent: 20px;
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#fypiqpxsxm .gt_indent_5 { #tapeacohhi .gt_indent_5 {
text-indent: 25px; text-indent: 25px;
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</style> </style>
@ -1065,23 +1067,23 @@ demonstration of the functions.</p>
</div> </div>
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r"> <div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">redcapcast_meta</span> <span class="op">|&gt;</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> <code class="sourceCode R"><span><span class="va">redcapcast_meta</span> <span class="op">|&gt;</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>
<div id="yakcmvvbbq" style="padding-left:0px;padding-right:0px;padding-top:10px;padding-bottom:10px;overflow-x:auto;overflow-y:auto;width:auto;height:auto;"> <div id="xreuzzriun" style="padding-left:0px;padding-right:0px;padding-top:10px;padding-bottom:10px;overflow-x:auto;overflow-y:auto;width:auto;height:auto;">
<style>#yakcmvvbbq table { <style>#xreuzzriun table {
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border-style: none; border-style: none;
} }
#yakcmvvbbq p { #xreuzzriun p {
margin: 0; margin: 0;
padding: 0; padding: 0;
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#yakcmvvbbq .gt_table { #xreuzzriun .gt_table {
display: table; display: table;
border-collapse: collapse; border-collapse: collapse;
line-height: normal; line-height: normal;
@ -1107,12 +1109,12 @@ demonstration of the functions.</p>
border-left-color: #D3D3D3; border-left-color: #D3D3D3;
} }
#yakcmvvbbq .gt_caption { #xreuzzriun .gt_caption {
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color: #333333; color: #333333;
font-size: 125%; font-size: 125%;
font-weight: initial; font-weight: initial;
@ -1124,7 +1126,7 @@ demonstration of the functions.</p>
border-bottom-width: 0; border-bottom-width: 0;
} }
#yakcmvvbbq .gt_subtitle { #xreuzzriun .gt_subtitle {
color: #333333; color: #333333;
font-size: 85%; font-size: 85%;
font-weight: initial; font-weight: initial;
@ -1136,7 +1138,7 @@ demonstration of the functions.</p>
border-top-width: 0; border-top-width: 0;
} }
#yakcmvvbbq .gt_heading { #xreuzzriun .gt_heading {
background-color: #FFFFFF; background-color: #FFFFFF;
text-align: center; text-align: center;
border-bottom-color: #FFFFFF; border-bottom-color: #FFFFFF;
@ -1148,13 +1150,13 @@ demonstration of the functions.</p>
border-right-color: #D3D3D3; border-right-color: #D3D3D3;
} }
#yakcmvvbbq .gt_bottom_border { #xreuzzriun .gt_bottom_border {
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border-top-width: 2px; border-top-width: 2px;
border-top-color: #D3D3D3; border-top-color: #D3D3D3;
@ -1169,7 +1171,7 @@ demonstration of the functions.</p>
border-right-color: #D3D3D3; border-right-color: #D3D3D3;
} }
#yakcmvvbbq .gt_col_heading { #xreuzzriun .gt_col_heading {
color: #333333; color: #333333;
background-color: #FFFFFF; background-color: #FFFFFF;
font-size: 100%; font-size: 100%;
@ -1189,7 +1191,7 @@ demonstration of the functions.</p>
overflow-x: hidden; overflow-x: hidden;
} }
#yakcmvvbbq .gt_column_spanner_outer { #xreuzzriun .gt_column_spanner_outer {
color: #333333; color: #333333;
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font-size: 100%; font-size: 100%;
@ -1201,15 +1203,15 @@ demonstration of the functions.</p>
padding-right: 4px; padding-right: 4px;
} }
#yakcmvvbbq .gt_column_spanner_outer:first-child { #xreuzzriun .gt_column_spanner_outer:first-child {
padding-left: 0; padding-left: 0;
} }
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border-bottom-style: solid; border-bottom-style: solid;
border-bottom-width: 2px; border-bottom-width: 2px;
border-bottom-color: #D3D3D3; border-bottom-color: #D3D3D3;
@ -1221,11 +1223,11 @@ demonstration of the functions.</p>
width: 100%; width: 100%;
} }
#yakcmvvbbq .gt_spanner_row { #xreuzzriun .gt_spanner_row {
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padding-left: 5px; padding-left: 5px;
@ -1251,7 +1253,7 @@ demonstration of the functions.</p>
text-align: left; text-align: left;
} }
#yakcmvvbbq .gt_empty_group_heading { #xreuzzriun .gt_empty_group_heading {
padding: 0.5px; padding: 0.5px;
color: #333333; color: #333333;
background-color: #FFFFFF; background-color: #FFFFFF;
@ -1266,15 +1268,15 @@ demonstration of the functions.</p>
vertical-align: middle; vertical-align: middle;
} }
#yakcmvvbbq .gt_from_md > :first-child { #xreuzzriun .gt_from_md > :first-child {
margin-top: 0; margin-top: 0;
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padding-left: 5px; padding-left: 5px;
@ -1293,7 +1295,7 @@ demonstration of the functions.</p>
overflow-x: hidden; overflow-x: hidden;
} }
#yakcmvvbbq .gt_stub { #xreuzzriun .gt_stub {
color: #333333; color: #333333;
background-color: #FFFFFF; background-color: #FFFFFF;
font-size: 100%; font-size: 100%;
@ -1306,7 +1308,7 @@ demonstration of the functions.</p>
padding-right: 5px; padding-right: 5px;
} }
#yakcmvvbbq .gt_stub_row_group { #xreuzzriun .gt_stub_row_group {
color: #333333; color: #333333;
background-color: #FFFFFF; background-color: #FFFFFF;
font-size: 100%; font-size: 100%;
@ -1320,15 +1322,15 @@ demonstration of the functions.</p>
vertical-align: top; vertical-align: top;
} }
#yakcmvvbbq .gt_row_group_first td { #xreuzzriun .gt_row_group_first td {
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color: #333333; color: #333333;
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@ -1338,16 +1340,16 @@ demonstration of the functions.</p>
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border-top-style: solid; border-top-style: solid;
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padding-top: 8px; padding-top: 8px;
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@ -1357,7 +1359,7 @@ demonstration of the functions.</p>
border-bottom-color: #D3D3D3; border-bottom-color: #D3D3D3;
} }
#yakcmvvbbq .gt_grand_summary_row { #xreuzzriun .gt_grand_summary_row {
color: #333333; color: #333333;
background-color: #FFFFFF; background-color: #FFFFFF;
text-transform: inherit; text-transform: inherit;
@ -1367,7 +1369,7 @@ demonstration of the functions.</p>
padding-right: 5px; padding-right: 5px;
} }
#yakcmvvbbq .gt_first_grand_summary_row { #xreuzzriun .gt_first_grand_summary_row {
padding-top: 8px; padding-top: 8px;
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padding-left: 5px; padding-left: 5px;
@ -1377,7 +1379,7 @@ demonstration of the functions.</p>
border-top-color: #D3D3D3; border-top-color: #D3D3D3;
} }
#yakcmvvbbq .gt_last_grand_summary_row_top { #xreuzzriun .gt_last_grand_summary_row_top {
padding-top: 8px; padding-top: 8px;
padding-bottom: 8px; padding-bottom: 8px;
padding-left: 5px; padding-left: 5px;
@ -1387,11 +1389,11 @@ demonstration of the functions.</p>
border-bottom-color: #D3D3D3; border-bottom-color: #D3D3D3;
} }
#yakcmvvbbq .gt_striped { #xreuzzriun .gt_striped {
background-color: rgba(128, 128, 128, 0.05); background-color: rgba(128, 128, 128, 0.05);
} }
#yakcmvvbbq .gt_table_body { #xreuzzriun .gt_table_body {
border-top-style: solid; border-top-style: solid;
border-top-width: 2px; border-top-width: 2px;
border-top-color: #D3D3D3; border-top-color: #D3D3D3;
@ -1400,7 +1402,7 @@ demonstration of the functions.</p>
border-bottom-color: #D3D3D3; border-bottom-color: #D3D3D3;
} }
#yakcmvvbbq .gt_footnotes { #xreuzzriun .gt_footnotes {
color: #333333; color: #333333;
background-color: #FFFFFF; background-color: #FFFFFF;
border-bottom-style: none; border-bottom-style: none;
@ -1414,7 +1416,7 @@ demonstration of the functions.</p>
border-right-color: #D3D3D3; border-right-color: #D3D3D3;
} }
#yakcmvvbbq .gt_footnote { #xreuzzriun .gt_footnote {
margin: 0px; margin: 0px;
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@ -1423,7 +1425,7 @@ demonstration of the functions.</p>
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@ -1437,7 +1439,7 @@ demonstration of the functions.</p>
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<img src="../logo.png" class="logo" alt=""><h1>Shiny-app</h1>
<small class="dont-index">Source: <a href="https://github.com/agdamsbo/REDCapCAST/blob/HEAD/vignettes/Shiny-app.Rmd" class="external-link"><code>vignettes/Shiny-app.Rmd</code></a></small>
<div class="d-none name"><code>Shiny-app.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>
<p>To make the easiest possible transistion from spreadsheet/dataset to
REDCap, I have created a small Shiny app, which adds a graphical
interface to the casting of a data dictionary and data upload. Install
the package and run the app as follows:</p>
<div class="sourceCode" id="cb2"><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">require</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>
<span><span class="fu"><a href="../reference/shiny_cast.html">shiny_cast</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
<p>The app will launch in a new window and the interface should be
fairly self-explanatory. The app only provides the most basic
functionality, but might be extended in the future.</p>
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@ -53,7 +55,11 @@
<h3>All vignettes</h3> <h3>All vignettes</h3>
<p class="section-desc"></p> <p class="section-desc"></p>
<dl><dt><a href="Introduction.html">Introduction</a></dt> <dl><dt><a href="Database-creation.html">Database-creation</a></dt>
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@ -7,10 +7,9 @@
<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"> <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
<meta name="description" content="Originally forked from the R part of REDCapRITS by Paul Egeler. <meta name="description" content="Originally forked from the R part of REDCapRITS by Paul Egeler.
See &lt;https://github.com/pegeler/REDCapRITS&gt;. See &lt;https://github.com/pegeler/REDCapRITS&gt;.
Handles castellated datasets from REDCap projects with repeating instruments. REDCap database casting and handling of castellated data when using
Assists in casting tidy tables from raw REDCap data exports for each repeated instruments and longitudinal projects. Keeps a focused data export
repeated instrument. Keeps a focused data export approach, by allowing to approach, by allowing to only export required data from the database.
only export required data from the database.
REDCap (Research Electronic Data Capture) is a secure, web-based software REDCap (Research Electronic Data Capture) is a secure, web-based software
platform designed to support data capture for research studies, providing platform designed to support data capture for research studies, providing
1) an intuitive interface for validated data capture; 2) audit trails for 1) an intuitive interface for validated data capture; 2) audit trails for
@ -33,10 +32,9 @@
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<meta property="og:description" content="Originally forked from the R part of REDCapRITS by Paul Egeler. <meta property="og:description" content="Originally forked from the R part of REDCapRITS by Paul Egeler.
See &lt;https://github.com/pegeler/REDCapRITS&gt;. See &lt;https://github.com/pegeler/REDCapRITS&gt;.
Handles castellated datasets from REDCap projects with repeating instruments. REDCap database casting and handling of castellated data when using
Assists in casting tidy tables from raw REDCap data exports for each repeated instruments and longitudinal projects. Keeps a focused data export
repeated instrument. Keeps a focused data export approach, by allowing to approach, by allowing to only export required data from the database.
only export required data from the database.
REDCap (Research Electronic Data Capture) is a secure, web-based software REDCap (Research Electronic Data Capture) is a secure, web-based software
platform designed to support data capture for research studies, providing platform designed to support data capture for research studies, providing
1) an intuitive interface for validated data capture; 2) audit trails for 1) an intuitive interface for validated data capture; 2) audit trails for
@ -74,7 +72,9 @@
<li class="nav-item dropdown"> <li class="nav-item dropdown">
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a> <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
<div class="dropdown-menu" aria-labelledby="dropdown-articles"> <div class="dropdown-menu" aria-labelledby="dropdown-articles">
<a class="dropdown-item" href="articles/Database-creation.html">Database-creation</a>
<a class="dropdown-item" href="articles/Introduction.html">Introduction</a> <a class="dropdown-item" href="articles/Introduction.html">Introduction</a>
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@ -105,25 +105,26 @@
<img src="logo.png" class="logo" alt=""><h1 id="redcapcast-package-">REDCapCAST package <a class="anchor" aria-label="anchor" href="#redcapcast-package-"></a> <img src="logo.png" class="logo" alt=""><h1 id="redcapcast-package-">REDCapCAST package <a class="anchor" aria-label="anchor" href="#redcapcast-package-"></a>
</h1> </h1>
</div> </div>
<p>REDCap Castellated data handling when using repeated instruments.</p> <p>REDCap database casting and handling of castellated data when using repeated instruments and longitudinal projects.</p>
<p>This package is a fork of <a href="https://github.com/pegeler/REDCapRITS" class="external-link">pegeler/REDCapRITS</a>. The REDCapRITS represents great and extensive work to handle castellated REDCap data in different programming languages. This fork is purely minded on R usage and includes a few implementations of the main <code>REDCap_split</code> function.</p> <p>This package is a fork of <a href="https://github.com/pegeler/REDCapRITS" class="external-link">pegeler/REDCapRITS</a>. The REDCapRITS represents great and extensive work to handle castellated REDCap data in different programming languages. This fork is purely minded on R usage and includes a few implementations of the main <code>REDCap_split</code> function.</p>
<p>The main goal for this project was to allow for a “minimal data” approach by allowing to filter records, instruments and variables in the export to only download data needed. I think this approach is desireable for handling sensitive, clinical data. No similar functionality is available from similar tools (like <code>REDCapR</code> or <code>REDCapTidieR</code>). Please refer to <a href="https://redcap-tools.github.io/" class="external-link">REDCap-Tools</a> for other great tools.</p> <p>This package is very much to be seen as an attempt at a R-to-REDCap-to-R foundry for handling both the transition from dataset/variable list to database and the other way, from REDCap database to a tidy dataset. The goal was also to allow for a “minimal data” approach by allowing to filter records, instruments and variables in the export to only download data needed. I think this approach is desirable for handling sensitive, clinical data. Please refer to <a href="https://redcap-tools.github.io/" class="external-link">REDCap-Tools</a> for other great tools for working with REDCap in R.</p>
<div class="section level2"> <div class="section level2">
<h2 id="use-and-immprovements">Use and immprovements<a class="anchor" aria-label="anchor" href="#use-and-immprovements"></a> <h2 id="use-and-immprovements">Use and immprovements<a class="anchor" aria-label="anchor" href="#use-and-immprovements"></a>
</h2> </h2>
<p>This package is primarily relevant for working with longitudinal projects and/or projects using repeated instruments. Here is just a short descirption of the main functions:</p> <p>Here is just a short description of the main functions:</p>
<ul> <ul>
<li><p><code>REDcap_split()</code>: Works largely as the original <code>REDCapRITS::REDCap_split()</code>. It takes a REDCap dataset and metadata (data dictionary) to split the data set into a list of dataframes of instruments.</p></li> <li><p><code>REDcap_split()</code>: Works largely as the original <code>REDCapRITS::REDCap_split()</code>. It takes a REDCap dataset and metadata (data dictionary) to split the data set into a list of dataframes of instruments.</p></li>
<li><p><code><a href="reference/read_redcap_tables.html">read_redcap_tables()</a></code>: wraps the use of <a href="https://github.com/OuhscBbmc/REDCapR" class="external-link"><code>REDCapR::redcap_read()</code></a> with <code><a href="reference/REDCap_split.html">REDCap_split()</a></code> to ease the export of REDCap data.</p></li> <li><p><code><a href="reference/read_redcap_tables.html">read_redcap_tables()</a></code>: wraps the use of <a href="https://github.com/OuhscBbmc/REDCapR" class="external-link"><code>REDCapR::redcap_read()</code></a> with <code><a href="reference/REDCap_split.html">REDCap_split()</a></code> to ease the export of REDCap data. Default output is a list of data frames with one data frame for each REDCap instrument.</p></li>
<li><p><code><a href="reference/redcap_wider.html">redcap_wider()</a></code>: pivots each data frame with repeated instruments to a wide format utilizing the <a href="https://tidyr.tidyverse.org/reference/pivot_wider.html" class="external-link"><code>tidyr::pivot_wider()</code></a> from the <a href="https://www.tidyverse.org/" class="external-link">tidyverse</a>.</p></li> <li><p><code><a href="reference/redcap_wider.html">redcap_wider()</a></code>: joins and pivots a list of data frames with repeated instruments to a wide format utilizing the <a href="https://tidyr.tidyverse.org/reference/pivot_wider.html" class="external-link"><code>tidyr::pivot_wider()</code></a> from the <a href="https://www.tidyverse.org/" class="external-link">tidyverse</a>.</p></li>
<li><p><code><a href="reference/easy_redcap.html">easy_redcap()</a></code>: combines secure API key storage with the <code>keyring</code>-package, focused data retrieval and optional widening. This is the recommended approach for easy data access and analysis.</p></li> <li><p><code><a href="reference/easy_redcap.html">easy_redcap()</a></code>: combines secure API key storage with the <code>keyring</code>-package, focused data retrieval and optional widening. This is the recommended approach for easy data access and analysis.</p></li>
<li><p><code><a href="reference/ds2dd_detailed.html">ds2dd_detailed()</a></code>: Converts a data set to a data dictionary for upload to a new REDCap database. Variables (fields) and instruments in a REDCap data base are defined by this data dictionary.</p></li>
<li><p><code><a href="reference/shiny_cast.html">shiny_cast()</a></code>: <a href="">Shiny</a> application to ease the process of converting a spreadsheet/data set to a REDCap database. The app runs locally and data is transferred securely. You can just create and upload the data dictionary, but you can also transfer the given data in the same process.</p></li>
</ul> </ul>
<p>Compared to the original <code>REDCapRITS</code>, all matching functions are improved to accept column naming of REDCap data from manual download or API export.</p>
</div> </div>
<div class="section level2"> <div class="section level2">
<h2 id="future">Future<a class="anchor" aria-label="anchor" href="#future"></a> <h2 id="future">Future<a class="anchor" aria-label="anchor" href="#future"></a>
</h2> </h2>
<p>The plan with this package is to be bundled with a Handbook on working with REDCap from R. I plan to also include functionality to assist in casting (yes, pun intended) the initial REDCap database.</p> <p>The plan with this package is to be bundled with a Handbook on working with REDCap from R. This work is in progress but is limited by the time available. Please feel free to contact me or create and issue with ideas for future additions.</p>
</div> </div>
<div class="section level2"> <div class="section level2">
<h2 id="installation">Installation<a class="anchor" aria-label="anchor" href="#installation"></a> <h2 id="installation">Installation<a class="anchor" aria-label="anchor" href="#installation"></a>

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<img src="../logo.png" class="logo" alt=""><h1>Deploy the Shiny app with rsconnect</h1>
<small class="dont-index">Source: <a href="https://github.com/agdamsbo/REDCapCAST/blob/HEAD/R/shiny_cast.R" class="external-link"><code>R/shiny_cast.R</code></a></small>
<div class="d-none name"><code>deploy_shiny.Rd</code></div>
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<p>Deploy the Shiny app with rsconnect</p>
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<div class="section level2">
<h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">deploy_shiny</span><span class="op">(</span>path <span class="op">=</span> <span class="fu">here</span><span class="fu">::</span><span class="fu"><a href="https://here.r-lib.org//reference/here.html" class="external-link">here</a></span><span class="op">(</span><span class="st">"app/"</span><span class="op">)</span>, name.app <span class="op">=</span> <span class="st">"shiny_cast"</span><span class="op">)</span></span></code></pre></div>
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<div class="section level2">
<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
<dl><dt>path</dt>
<dd><p>app folder path</p></dd>
<dt>name.app</dt>
<dd><p>name of deployed app</p></dd>
</dl></div>
<div class="section level2">
<h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
<p>deploy</p>
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<div class="section level2">
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># deploy_shiny</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"></span>
</code></pre></div>
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@ -77,6 +79,11 @@
<dd>Convert single digits to words</dd> <dd>Convert single digits to words</dd>
</dl><dl><dt> </dl><dl><dt>
<code><a href="deploy_shiny.html">deploy_shiny()</a></code>
</dt>
<dd>Deploy the Shiny app with rsconnect</dd>
</dl><dl><dt>
<code><a href="ds2dd.html">ds2dd()</a></code> <code><a href="ds2dd.html">ds2dd()</a></code>
</dt> </dt>
<dd>(DEPRECATED) Data set to data dictionary function</dd> <dd>(DEPRECATED) Data set to data dictionary function</dd>
@ -137,6 +144,11 @@
<dd>Match fields to forms</dd> <dd>Match fields to forms</dd>
</dl><dl><dt> </dl><dl><dt>
<code><a href="mtcars_redcap.html">mtcars_redcap</a></code>
</dt>
<dd>mtcars dataset slightly modified to use for Shiny app upload demonstration</dd>
</dl><dl><dt>
<code><a href="read_input.html">read_input()</a></code> <code><a href="read_input.html">read_input()</a></code>
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<img src="../logo.png" class="logo" alt=""><h1>mtcars dataset slightly modified to use for Shiny app upload demonstration</h1>
<small class="dont-index">Source: <a href="https://github.com/agdamsbo/REDCapCAST/blob/HEAD/R/mtcars_redcap.R" class="external-link"><code>R/mtcars_redcap.R</code></a></small>
<div class="d-none name"><code>mtcars_redcap.Rd</code></div>
</div>
<div class="ref-description section level2">
<p>mtcars dataset slightly modified to use for Shiny app upload demonstration</p>
</div>
<div class="section level2">
<h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><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="va">mtcars_redcap</span><span class="op">)</span></span></code></pre></div>
</div>
<div class="section level2">
<h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
<p>A data frame with 13 variables:</p><dl><dt>record_id</dt>
<dd><p>ID, numeric</p></dd>
<dt>mpg</dt>
<dd><p>ID, numeric</p></dd>
<dt>cyl</dt>
<dd><p>ID, numeric</p></dd>
<dt>disp</dt>
<dd><p>ID, numeric</p></dd>
<dt>hp</dt>
<dd><p>ID, numeric</p></dd>
<dt>drat</dt>
<dd><p>ID, numeric</p></dd>
<dt>wt</dt>
<dd><p>ID, numeric</p></dd>
<dt>qsec</dt>
<dd><p>ID, numeric</p></dd>
<dt>vs</dt>
<dd><p>ID, numeric</p></dd>
<dt>am</dt>
<dd><p>ID, numeric</p></dd>
<dt>gear</dt>
<dd><p>ID, numeric</p></dd>
<dt>carb</dt>
<dd><p>ID, numeric</p></dd>
<dt>name</dt>
<dd><p>original rownames, charater</p></dd>
</dl></div>
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