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<main id="main" class="col-md-9"><div class="page-header">
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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 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 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/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>
|
||||
</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>
|
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<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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</div>
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<p>Developed by Andreas Gammelgaard Damsbo, Paul Egeler.</p>
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<a class="dropdown-item" href="../articles/Database-creation.html">Database-creation</a>
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<a class="dropdown-item" href="../articles/Introduction.html">Introduction</a>
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<a class="dropdown-item" href="../articles/Shiny-app.html">Shiny-app</a>
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<li class="nav-item">
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@ -98,23 +100,23 @@ demonstration of the functions.</p>
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</h2>
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<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="va">redcapcast_data</span> <span class="op">|></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="fypiqpxsxm" style="padding-left:0px;padding-right:0px;padding-top:10px;padding-bottom:10px;overflow-x:auto;overflow-y:auto;width:auto;height:auto;">
|
||||
<style>#fypiqpxsxm table {
|
||||
<div id="tapeacohhi" style="padding-left:0px;padding-right:0px;padding-top:10px;padding-bottom:10px;overflow-x:auto;overflow-y:auto;width:auto;height:auto;">
|
||||
<style>#tapeacohhi table {
|
||||
font-family: system-ui, 'Segoe UI', Roboto, Helvetica, Arial, sans-serif, 'Apple Color Emoji', 'Segoe UI Emoji', 'Segoe UI Symbol', 'Noto Color Emoji';
|
||||
-webkit-font-smoothing: antialiased;
|
||||
-moz-osx-font-smoothing: grayscale;
|
||||
}
|
||||
|
||||
#fypiqpxsxm thead, #fypiqpxsxm tbody, #fypiqpxsxm tfoot, #fypiqpxsxm tr, #fypiqpxsxm td, #fypiqpxsxm th {
|
||||
#tapeacohhi thead, #tapeacohhi tbody, #tapeacohhi tfoot, #tapeacohhi tr, #tapeacohhi td, #tapeacohhi th {
|
||||
border-style: none;
|
||||
}
|
||||
|
||||
#fypiqpxsxm p {
|
||||
#tapeacohhi p {
|
||||
margin: 0;
|
||||
padding: 0;
|
||||
}
|
||||
|
||||
#fypiqpxsxm .gt_table {
|
||||
#tapeacohhi .gt_table {
|
||||
display: table;
|
||||
border-collapse: collapse;
|
||||
line-height: normal;
|
||||
@ -140,12 +142,12 @@ demonstration of the functions.</p>
|
||||
border-left-color: #D3D3D3;
|
||||
}
|
||||
|
||||
#fypiqpxsxm .gt_caption {
|
||||
#tapeacohhi .gt_caption {
|
||||
padding-top: 4px;
|
||||
padding-bottom: 4px;
|
||||
}
|
||||
|
||||
#fypiqpxsxm .gt_title {
|
||||
#tapeacohhi .gt_title {
|
||||
color: #333333;
|
||||
font-size: 125%;
|
||||
font-weight: initial;
|
||||
@ -157,7 +159,7 @@ demonstration of the functions.</p>
|
||||
border-bottom-width: 0;
|
||||
}
|
||||
|
||||
#fypiqpxsxm .gt_subtitle {
|
||||
#tapeacohhi .gt_subtitle {
|
||||
color: #333333;
|
||||
font-size: 85%;
|
||||
font-weight: initial;
|
||||
@ -169,7 +171,7 @@ demonstration of the functions.</p>
|
||||
border-top-width: 0;
|
||||
}
|
||||
|
||||
#fypiqpxsxm .gt_heading {
|
||||
#tapeacohhi .gt_heading {
|
||||
background-color: #FFFFFF;
|
||||
text-align: center;
|
||||
border-bottom-color: #FFFFFF;
|
||||
@ -181,13 +183,13 @@ demonstration of the functions.</p>
|
||||
border-right-color: #D3D3D3;
|
||||
}
|
||||
|
||||
#fypiqpxsxm .gt_bottom_border {
|
||||
#tapeacohhi .gt_bottom_border {
|
||||
border-bottom-style: solid;
|
||||
border-bottom-width: 2px;
|
||||
border-bottom-color: #D3D3D3;
|
||||
}
|
||||
|
||||
#fypiqpxsxm .gt_col_headings {
|
||||
#tapeacohhi .gt_col_headings {
|
||||
border-top-style: solid;
|
||||
border-top-width: 2px;
|
||||
border-top-color: #D3D3D3;
|
||||
@ -202,7 +204,7 @@ demonstration of the functions.</p>
|
||||
border-right-color: #D3D3D3;
|
||||
}
|
||||
|
||||
#fypiqpxsxm .gt_col_heading {
|
||||
#tapeacohhi .gt_col_heading {
|
||||
color: #333333;
|
||||
background-color: #FFFFFF;
|
||||
font-size: 100%;
|
||||
@ -222,7 +224,7 @@ demonstration of the functions.</p>
|
||||
overflow-x: hidden;
|
||||
}
|
||||
|
||||
#fypiqpxsxm .gt_column_spanner_outer {
|
||||
#tapeacohhi .gt_column_spanner_outer {
|
||||
color: #333333;
|
||||
background-color: #FFFFFF;
|
||||
font-size: 100%;
|
||||
@ -234,15 +236,15 @@ demonstration of the functions.</p>
|
||||
padding-right: 4px;
|
||||
}
|
||||
|
||||
#fypiqpxsxm .gt_column_spanner_outer:first-child {
|
||||
#tapeacohhi .gt_column_spanner_outer:first-child {
|
||||
padding-left: 0;
|
||||
}
|
||||
|
||||
#fypiqpxsxm .gt_column_spanner_outer:last-child {
|
||||
#tapeacohhi .gt_column_spanner_outer:last-child {
|
||||
padding-right: 0;
|
||||
}
|
||||
|
||||
#fypiqpxsxm .gt_column_spanner {
|
||||
#tapeacohhi .gt_column_spanner {
|
||||
border-bottom-style: solid;
|
||||
border-bottom-width: 2px;
|
||||
border-bottom-color: #D3D3D3;
|
||||
@ -254,11 +256,11 @@ demonstration of the functions.</p>
|
||||
width: 100%;
|
||||
}
|
||||
|
||||
#fypiqpxsxm .gt_spanner_row {
|
||||
#tapeacohhi .gt_spanner_row {
|
||||
border-bottom-style: hidden;
|
||||
}
|
||||
|
||||
#fypiqpxsxm .gt_group_heading {
|
||||
#tapeacohhi .gt_group_heading {
|
||||
padding-top: 8px;
|
||||
padding-bottom: 8px;
|
||||
padding-left: 5px;
|
||||
@ -284,7 +286,7 @@ demonstration of the functions.</p>
|
||||
text-align: left;
|
||||
}
|
||||
|
||||
#fypiqpxsxm .gt_empty_group_heading {
|
||||
#tapeacohhi .gt_empty_group_heading {
|
||||
padding: 0.5px;
|
||||
color: #333333;
|
||||
background-color: #FFFFFF;
|
||||
@ -299,15 +301,15 @@ demonstration of the functions.</p>
|
||||
vertical-align: middle;
|
||||
}
|
||||
|
||||
#fypiqpxsxm .gt_from_md > :first-child {
|
||||
#tapeacohhi .gt_from_md > :first-child {
|
||||
margin-top: 0;
|
||||
}
|
||||
|
||||
#fypiqpxsxm .gt_from_md > :last-child {
|
||||
#tapeacohhi .gt_from_md > :last-child {
|
||||
margin-bottom: 0;
|
||||
}
|
||||
|
||||
#fypiqpxsxm .gt_row {
|
||||
#tapeacohhi .gt_row {
|
||||
padding-top: 8px;
|
||||
padding-bottom: 8px;
|
||||
padding-left: 5px;
|
||||
@ -326,7 +328,7 @@ demonstration of the functions.</p>
|
||||
overflow-x: hidden;
|
||||
}
|
||||
|
||||
#fypiqpxsxm .gt_stub {
|
||||
#tapeacohhi .gt_stub {
|
||||
color: #333333;
|
||||
background-color: #FFFFFF;
|
||||
font-size: 100%;
|
||||
@ -339,7 +341,7 @@ demonstration of the functions.</p>
|
||||
padding-right: 5px;
|
||||
}
|
||||
|
||||
#fypiqpxsxm .gt_stub_row_group {
|
||||
#tapeacohhi .gt_stub_row_group {
|
||||
color: #333333;
|
||||
background-color: #FFFFFF;
|
||||
font-size: 100%;
|
||||
@ -353,15 +355,15 @@ demonstration of the functions.</p>
|
||||
vertical-align: top;
|
||||
}
|
||||
|
||||
#fypiqpxsxm .gt_row_group_first td {
|
||||
#tapeacohhi .gt_row_group_first td {
|
||||
border-top-width: 2px;
|
||||
}
|
||||
|
||||
#fypiqpxsxm .gt_row_group_first th {
|
||||
#tapeacohhi .gt_row_group_first th {
|
||||
border-top-width: 2px;
|
||||
}
|
||||
|
||||
#fypiqpxsxm .gt_summary_row {
|
||||
#tapeacohhi .gt_summary_row {
|
||||
color: #333333;
|
||||
background-color: #FFFFFF;
|
||||
text-transform: inherit;
|
||||
@ -371,16 +373,16 @@ demonstration of the functions.</p>
|
||||
padding-right: 5px;
|
||||
}
|
||||
|
||||
#fypiqpxsxm .gt_first_summary_row {
|
||||
#tapeacohhi .gt_first_summary_row {
|
||||
border-top-style: solid;
|
||||
border-top-color: #D3D3D3;
|
||||
}
|
||||
|
||||
#fypiqpxsxm .gt_first_summary_row.thick {
|
||||
#tapeacohhi .gt_first_summary_row.thick {
|
||||
border-top-width: 2px;
|
||||
}
|
||||
|
||||
#fypiqpxsxm .gt_last_summary_row {
|
||||
#tapeacohhi .gt_last_summary_row {
|
||||
padding-top: 8px;
|
||||
padding-bottom: 8px;
|
||||
padding-left: 5px;
|
||||
@ -390,7 +392,7 @@ demonstration of the functions.</p>
|
||||
border-bottom-color: #D3D3D3;
|
||||
}
|
||||
|
||||
#fypiqpxsxm .gt_grand_summary_row {
|
||||
#tapeacohhi .gt_grand_summary_row {
|
||||
color: #333333;
|
||||
background-color: #FFFFFF;
|
||||
text-transform: inherit;
|
||||
@ -400,7 +402,7 @@ demonstration of the functions.</p>
|
||||
padding-right: 5px;
|
||||
}
|
||||
|
||||
#fypiqpxsxm .gt_first_grand_summary_row {
|
||||
#tapeacohhi .gt_first_grand_summary_row {
|
||||
padding-top: 8px;
|
||||
padding-bottom: 8px;
|
||||
padding-left: 5px;
|
||||
@ -410,7 +412,7 @@ demonstration of the functions.</p>
|
||||
border-top-color: #D3D3D3;
|
||||
}
|
||||
|
||||
#fypiqpxsxm .gt_last_grand_summary_row_top {
|
||||
#tapeacohhi .gt_last_grand_summary_row_top {
|
||||
padding-top: 8px;
|
||||
padding-bottom: 8px;
|
||||
padding-left: 5px;
|
||||
@ -420,11 +422,11 @@ demonstration of the functions.</p>
|
||||
border-bottom-color: #D3D3D3;
|
||||
}
|
||||
|
||||
#fypiqpxsxm .gt_striped {
|
||||
#tapeacohhi .gt_striped {
|
||||
background-color: rgba(128, 128, 128, 0.05);
|
||||
}
|
||||
|
||||
#fypiqpxsxm .gt_table_body {
|
||||
#tapeacohhi .gt_table_body {
|
||||
border-top-style: solid;
|
||||
border-top-width: 2px;
|
||||
border-top-color: #D3D3D3;
|
||||
@ -433,7 +435,7 @@ demonstration of the functions.</p>
|
||||
border-bottom-color: #D3D3D3;
|
||||
}
|
||||
|
||||
#fypiqpxsxm .gt_footnotes {
|
||||
#tapeacohhi .gt_footnotes {
|
||||
color: #333333;
|
||||
background-color: #FFFFFF;
|
||||
border-bottom-style: none;
|
||||
@ -447,7 +449,7 @@ demonstration of the functions.</p>
|
||||
border-right-color: #D3D3D3;
|
||||
}
|
||||
|
||||
#fypiqpxsxm .gt_footnote {
|
||||
#tapeacohhi .gt_footnote {
|
||||
margin: 0px;
|
||||
font-size: 90%;
|
||||
padding-top: 4px;
|
||||
@ -456,7 +458,7 @@ demonstration of the functions.</p>
|
||||
padding-right: 5px;
|
||||
}
|
||||
|
||||
#fypiqpxsxm .gt_sourcenotes {
|
||||
#tapeacohhi .gt_sourcenotes {
|
||||
color: #333333;
|
||||
background-color: #FFFFFF;
|
||||
border-bottom-style: none;
|
||||
@ -470,7 +472,7 @@ demonstration of the functions.</p>
|
||||
border-right-color: #D3D3D3;
|
||||
}
|
||||
|
||||
#fypiqpxsxm .gt_sourcenote {
|
||||
#tapeacohhi .gt_sourcenote {
|
||||
font-size: 90%;
|
||||
padding-top: 4px;
|
||||
padding-bottom: 4px;
|
||||
@ -478,63 +480,63 @@ demonstration of the functions.</p>
|
||||
padding-right: 5px;
|
||||
}
|
||||
|
||||
#fypiqpxsxm .gt_left {
|
||||
#tapeacohhi .gt_left {
|
||||
text-align: left;
|
||||
}
|
||||
|
||||
#fypiqpxsxm .gt_center {
|
||||
#tapeacohhi .gt_center {
|
||||
text-align: center;
|
||||
}
|
||||
|
||||
#fypiqpxsxm .gt_right {
|
||||
#tapeacohhi .gt_right {
|
||||
text-align: right;
|
||||
font-variant-numeric: tabular-nums;
|
||||
}
|
||||
|
||||
#fypiqpxsxm .gt_font_normal {
|
||||
#tapeacohhi .gt_font_normal {
|
||||
font-weight: normal;
|
||||
}
|
||||
|
||||
#fypiqpxsxm .gt_font_bold {
|
||||
#tapeacohhi .gt_font_bold {
|
||||
font-weight: bold;
|
||||
}
|
||||
|
||||
#fypiqpxsxm .gt_font_italic {
|
||||
#tapeacohhi .gt_font_italic {
|
||||
font-style: italic;
|
||||
}
|
||||
|
||||
#fypiqpxsxm .gt_super {
|
||||
#tapeacohhi .gt_super {
|
||||
font-size: 65%;
|
||||
}
|
||||
|
||||
#fypiqpxsxm .gt_footnote_marks {
|
||||
#tapeacohhi .gt_footnote_marks {
|
||||
font-size: 75%;
|
||||
vertical-align: 0.4em;
|
||||
position: initial;
|
||||
}
|
||||
|
||||
#fypiqpxsxm .gt_asterisk {
|
||||
#tapeacohhi .gt_asterisk {
|
||||
font-size: 100%;
|
||||
vertical-align: 0;
|
||||
}
|
||||
|
||||
#fypiqpxsxm .gt_indent_1 {
|
||||
#tapeacohhi .gt_indent_1 {
|
||||
text-indent: 5px;
|
||||
}
|
||||
|
||||
#fypiqpxsxm .gt_indent_2 {
|
||||
#tapeacohhi .gt_indent_2 {
|
||||
text-indent: 10px;
|
||||
}
|
||||
|
||||
#fypiqpxsxm .gt_indent_3 {
|
||||
#tapeacohhi .gt_indent_3 {
|
||||
text-indent: 15px;
|
||||
}
|
||||
|
||||
#fypiqpxsxm .gt_indent_4 {
|
||||
#tapeacohhi .gt_indent_4 {
|
||||
text-indent: 20px;
|
||||
}
|
||||
|
||||
#fypiqpxsxm .gt_indent_5 {
|
||||
#tapeacohhi .gt_indent_5 {
|
||||
text-indent: 25px;
|
||||
}
|
||||
</style>
|
||||
@ -1065,23 +1067,23 @@ demonstration of the functions.</p>
|
||||
</div>
|
||||
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="va">redcapcast_meta</span> <span class="op">|></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;">
|
||||
<style>#yakcmvvbbq table {
|
||||
<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>#xreuzzriun table {
|
||||
font-family: system-ui, 'Segoe UI', Roboto, Helvetica, Arial, sans-serif, 'Apple Color Emoji', 'Segoe UI Emoji', 'Segoe UI Symbol', 'Noto Color Emoji';
|
||||
-webkit-font-smoothing: antialiased;
|
||||
-moz-osx-font-smoothing: grayscale;
|
||||
}
|
||||
|
||||
#yakcmvvbbq thead, #yakcmvvbbq tbody, #yakcmvvbbq tfoot, #yakcmvvbbq tr, #yakcmvvbbq td, #yakcmvvbbq th {
|
||||
#xreuzzriun thead, #xreuzzriun tbody, #xreuzzriun tfoot, #xreuzzriun tr, #xreuzzriun td, #xreuzzriun th {
|
||||
border-style: none;
|
||||
}
|
||||
|
||||
#yakcmvvbbq p {
|
||||
#xreuzzriun p {
|
||||
margin: 0;
|
||||
padding: 0;
|
||||
}
|
||||
|
||||
#yakcmvvbbq .gt_table {
|
||||
#xreuzzriun .gt_table {
|
||||
display: table;
|
||||
border-collapse: collapse;
|
||||
line-height: normal;
|
||||
@ -1107,12 +1109,12 @@ demonstration of the functions.</p>
|
||||
border-left-color: #D3D3D3;
|
||||
}
|
||||
|
||||
#yakcmvvbbq .gt_caption {
|
||||
#xreuzzriun .gt_caption {
|
||||
padding-top: 4px;
|
||||
padding-bottom: 4px;
|
||||
}
|
||||
|
||||
#yakcmvvbbq .gt_title {
|
||||
#xreuzzriun .gt_title {
|
||||
color: #333333;
|
||||
font-size: 125%;
|
||||
font-weight: initial;
|
||||
@ -1124,7 +1126,7 @@ demonstration of the functions.</p>
|
||||
border-bottom-width: 0;
|
||||
}
|
||||
|
||||
#yakcmvvbbq .gt_subtitle {
|
||||
#xreuzzriun .gt_subtitle {
|
||||
color: #333333;
|
||||
font-size: 85%;
|
||||
font-weight: initial;
|
||||
@ -1136,7 +1138,7 @@ demonstration of the functions.</p>
|
||||
border-top-width: 0;
|
||||
}
|
||||
|
||||
#yakcmvvbbq .gt_heading {
|
||||
#xreuzzriun .gt_heading {
|
||||
background-color: #FFFFFF;
|
||||
text-align: center;
|
||||
border-bottom-color: #FFFFFF;
|
||||
@ -1148,13 +1150,13 @@ demonstration of the functions.</p>
|
||||
border-right-color: #D3D3D3;
|
||||
}
|
||||
|
||||
#yakcmvvbbq .gt_bottom_border {
|
||||
#xreuzzriun .gt_bottom_border {
|
||||
border-bottom-style: solid;
|
||||
border-bottom-width: 2px;
|
||||
border-bottom-color: #D3D3D3;
|
||||
}
|
||||
|
||||
#yakcmvvbbq .gt_col_headings {
|
||||
#xreuzzriun .gt_col_headings {
|
||||
border-top-style: solid;
|
||||
border-top-width: 2px;
|
||||
border-top-color: #D3D3D3;
|
||||
@ -1169,7 +1171,7 @@ demonstration of the functions.</p>
|
||||
border-right-color: #D3D3D3;
|
||||
}
|
||||
|
||||
#yakcmvvbbq .gt_col_heading {
|
||||
#xreuzzriun .gt_col_heading {
|
||||
color: #333333;
|
||||
background-color: #FFFFFF;
|
||||
font-size: 100%;
|
||||
@ -1189,7 +1191,7 @@ demonstration of the functions.</p>
|
||||
overflow-x: hidden;
|
||||
}
|
||||
|
||||
#yakcmvvbbq .gt_column_spanner_outer {
|
||||
#xreuzzriun .gt_column_spanner_outer {
|
||||
color: #333333;
|
||||
background-color: #FFFFFF;
|
||||
font-size: 100%;
|
||||
@ -1201,15 +1203,15 @@ demonstration of the functions.</p>
|
||||
padding-right: 4px;
|
||||
}
|
||||
|
||||
#yakcmvvbbq .gt_column_spanner_outer:first-child {
|
||||
#xreuzzriun .gt_column_spanner_outer:first-child {
|
||||
padding-left: 0;
|
||||
}
|
||||
|
||||
#yakcmvvbbq .gt_column_spanner_outer:last-child {
|
||||
#xreuzzriun .gt_column_spanner_outer:last-child {
|
||||
padding-right: 0;
|
||||
}
|
||||
|
||||
#yakcmvvbbq .gt_column_spanner {
|
||||
#xreuzzriun .gt_column_spanner {
|
||||
border-bottom-style: solid;
|
||||
border-bottom-width: 2px;
|
||||
border-bottom-color: #D3D3D3;
|
||||
@ -1221,11 +1223,11 @@ demonstration of the functions.</p>
|
||||
width: 100%;
|
||||
}
|
||||
|
||||
#yakcmvvbbq .gt_spanner_row {
|
||||
#xreuzzriun .gt_spanner_row {
|
||||
border-bottom-style: hidden;
|
||||
}
|
||||
|
||||
#yakcmvvbbq .gt_group_heading {
|
||||
#xreuzzriun .gt_group_heading {
|
||||
padding-top: 8px;
|
||||
padding-bottom: 8px;
|
||||
padding-left: 5px;
|
||||
@ -1251,7 +1253,7 @@ demonstration of the functions.</p>
|
||||
text-align: left;
|
||||
}
|
||||
|
||||
#yakcmvvbbq .gt_empty_group_heading {
|
||||
#xreuzzriun .gt_empty_group_heading {
|
||||
padding: 0.5px;
|
||||
color: #333333;
|
||||
background-color: #FFFFFF;
|
||||
@ -1266,15 +1268,15 @@ demonstration of the functions.</p>
|
||||
vertical-align: middle;
|
||||
}
|
||||
|
||||
#yakcmvvbbq .gt_from_md > :first-child {
|
||||
#xreuzzriun .gt_from_md > :first-child {
|
||||
margin-top: 0;
|
||||
}
|
||||
|
||||
#yakcmvvbbq .gt_from_md > :last-child {
|
||||
#xreuzzriun .gt_from_md > :last-child {
|
||||
margin-bottom: 0;
|
||||
}
|
||||
|
||||
#yakcmvvbbq .gt_row {
|
||||
#xreuzzriun .gt_row {
|
||||
padding-top: 8px;
|
||||
padding-bottom: 8px;
|
||||
padding-left: 5px;
|
||||
@ -1293,7 +1295,7 @@ demonstration of the functions.</p>
|
||||
overflow-x: hidden;
|
||||
}
|
||||
|
||||
#yakcmvvbbq .gt_stub {
|
||||
#xreuzzriun .gt_stub {
|
||||
color: #333333;
|
||||
background-color: #FFFFFF;
|
||||
font-size: 100%;
|
||||
@ -1306,7 +1308,7 @@ demonstration of the functions.</p>
|
||||
padding-right: 5px;
|
||||
}
|
||||
|
||||
#yakcmvvbbq .gt_stub_row_group {
|
||||
#xreuzzriun .gt_stub_row_group {
|
||||
color: #333333;
|
||||
background-color: #FFFFFF;
|
||||
font-size: 100%;
|
||||
@ -1320,15 +1322,15 @@ demonstration of the functions.</p>
|
||||
vertical-align: top;
|
||||
}
|
||||
|
||||
#yakcmvvbbq .gt_row_group_first td {
|
||||
#xreuzzriun .gt_row_group_first td {
|
||||
border-top-width: 2px;
|
||||
}
|
||||
|
||||
#yakcmvvbbq .gt_row_group_first th {
|
||||
#xreuzzriun .gt_row_group_first th {
|
||||
border-top-width: 2px;
|
||||
}
|
||||
|
||||
#yakcmvvbbq .gt_summary_row {
|
||||
#xreuzzriun .gt_summary_row {
|
||||
color: #333333;
|
||||
background-color: #FFFFFF;
|
||||
text-transform: inherit;
|
||||
@ -1338,16 +1340,16 @@ demonstration of the functions.</p>
|
||||
padding-right: 5px;
|
||||
}
|
||||
|
||||
#yakcmvvbbq .gt_first_summary_row {
|
||||
#xreuzzriun .gt_first_summary_row {
|
||||
border-top-style: solid;
|
||||
border-top-color: #D3D3D3;
|
||||
}
|
||||
|
||||
#yakcmvvbbq .gt_first_summary_row.thick {
|
||||
#xreuzzriun .gt_first_summary_row.thick {
|
||||
border-top-width: 2px;
|
||||
}
|
||||
|
||||
#yakcmvvbbq .gt_last_summary_row {
|
||||
#xreuzzriun .gt_last_summary_row {
|
||||
padding-top: 8px;
|
||||
padding-bottom: 8px;
|
||||
padding-left: 5px;
|
||||
@ -1357,7 +1359,7 @@ demonstration of the functions.</p>
|
||||
border-bottom-color: #D3D3D3;
|
||||
}
|
||||
|
||||
#yakcmvvbbq .gt_grand_summary_row {
|
||||
#xreuzzriun .gt_grand_summary_row {
|
||||
color: #333333;
|
||||
background-color: #FFFFFF;
|
||||
text-transform: inherit;
|
||||
@ -1367,7 +1369,7 @@ demonstration of the functions.</p>
|
||||
padding-right: 5px;
|
||||
}
|
||||
|
||||
#yakcmvvbbq .gt_first_grand_summary_row {
|
||||
#xreuzzriun .gt_first_grand_summary_row {
|
||||
padding-top: 8px;
|
||||
padding-bottom: 8px;
|
||||
padding-left: 5px;
|
||||
@ -1377,7 +1379,7 @@ demonstration of the functions.</p>
|
||||
border-top-color: #D3D3D3;
|
||||
}
|
||||
|
||||
#yakcmvvbbq .gt_last_grand_summary_row_top {
|
||||
#xreuzzriun .gt_last_grand_summary_row_top {
|
||||
padding-top: 8px;
|
||||
padding-bottom: 8px;
|
||||
padding-left: 5px;
|
||||
@ -1387,11 +1389,11 @@ demonstration of the functions.</p>
|
||||
border-bottom-color: #D3D3D3;
|
||||
}
|
||||
|
||||
#yakcmvvbbq .gt_striped {
|
||||
#xreuzzriun .gt_striped {
|
||||
background-color: rgba(128, 128, 128, 0.05);
|
||||
}
|
||||
|
||||
#yakcmvvbbq .gt_table_body {
|
||||
#xreuzzriun .gt_table_body {
|
||||
border-top-style: solid;
|
||||
border-top-width: 2px;
|
||||
border-top-color: #D3D3D3;
|
||||
@ -1400,7 +1402,7 @@ demonstration of the functions.</p>
|
||||
border-bottom-color: #D3D3D3;
|
||||
}
|
||||
|
||||
#yakcmvvbbq .gt_footnotes {
|
||||
#xreuzzriun .gt_footnotes {
|
||||
color: #333333;
|
||||
background-color: #FFFFFF;
|
||||
border-bottom-style: none;
|
||||
@ -1414,7 +1416,7 @@ demonstration of the functions.</p>
|
||||
border-right-color: #D3D3D3;
|
||||
}
|
||||
|
||||
#yakcmvvbbq .gt_footnote {
|
||||
#xreuzzriun .gt_footnote {
|
||||
margin: 0px;
|
||||
font-size: 90%;
|
||||
padding-top: 4px;
|
||||
@ -1423,7 +1425,7 @@ demonstration of the functions.</p>
|
||||
padding-right: 5px;
|
||||
}
|
||||
|
||||
#yakcmvvbbq .gt_sourcenotes {
|
||||
#xreuzzriun .gt_sourcenotes {
|
||||
color: #333333;
|
||||
background-color: #FFFFFF;
|
||||
border-bottom-style: none;
|
||||
@ -1437,7 +1439,7 @@ demonstration of the functions.</p>
|
||||
border-right-color: #D3D3D3;
|
||||
}
|
||||
|
||||
#yakcmvvbbq .gt_sourcenote {
|
||||
#xreuzzriun .gt_sourcenote {
|
||||
font-size: 90%;
|
||||
padding-top: 4px;
|
||||
padding-bottom: 4px;
|
||||
@ -1445,63 +1447,63 @@ demonstration of the functions.</p>
|
||||
padding-right: 5px;
|
||||
}
|
||||
|
||||
#yakcmvvbbq .gt_left {
|
||||
#xreuzzriun .gt_left {
|
||||
text-align: left;
|
||||
}
|
||||
|
||||
#yakcmvvbbq .gt_center {
|
||||
#xreuzzriun .gt_center {
|
||||
text-align: center;
|
||||
}
|
||||
|
||||
#yakcmvvbbq .gt_right {
|
||||
#xreuzzriun .gt_right {
|
||||
text-align: right;
|
||||
font-variant-numeric: tabular-nums;
|
||||
}
|
||||
|
||||
#yakcmvvbbq .gt_font_normal {
|
||||
#xreuzzriun .gt_font_normal {
|
||||
font-weight: normal;
|
||||
}
|
||||
|
||||
#yakcmvvbbq .gt_font_bold {
|
||||
#xreuzzriun .gt_font_bold {
|
||||
font-weight: bold;
|
||||
}
|
||||
|
||||
#yakcmvvbbq .gt_font_italic {
|
||||
#xreuzzriun .gt_font_italic {
|
||||
font-style: italic;
|
||||
}
|
||||
|
||||
#yakcmvvbbq .gt_super {
|
||||
#xreuzzriun .gt_super {
|
||||
font-size: 65%;
|
||||
}
|
||||
|
||||
#yakcmvvbbq .gt_footnote_marks {
|
||||
#xreuzzriun .gt_footnote_marks {
|
||||
font-size: 75%;
|
||||
vertical-align: 0.4em;
|
||||
position: initial;
|
||||
}
|
||||
|
||||
#yakcmvvbbq .gt_asterisk {
|
||||
#xreuzzriun .gt_asterisk {
|
||||
font-size: 100%;
|
||||
vertical-align: 0;
|
||||
}
|
||||
|
||||
#yakcmvvbbq .gt_indent_1 {
|
||||
#xreuzzriun .gt_indent_1 {
|
||||
text-indent: 5px;
|
||||
}
|
||||
|
||||
#yakcmvvbbq .gt_indent_2 {
|
||||
#xreuzzriun .gt_indent_2 {
|
||||
text-indent: 10px;
|
||||
}
|
||||
|
||||
#yakcmvvbbq .gt_indent_3 {
|
||||
#xreuzzriun .gt_indent_3 {
|
||||
text-indent: 15px;
|
||||
}
|
||||
|
||||
#yakcmvvbbq .gt_indent_4 {
|
||||
#xreuzzriun .gt_indent_4 {
|
||||
text-indent: 20px;
|
||||
}
|
||||
|
||||
#yakcmvvbbq .gt_indent_5 {
|
||||
#xreuzzriun .gt_indent_5 {
|
||||
text-indent: 25px;
|
||||
}
|
||||
</style>
|
||||
|
||||
127
articles/Shiny-app.html
Normal file
127
articles/Shiny-app.html
Normal file
@ -0,0 +1,127 @@
|
||||
<!DOCTYPE html>
|
||||
<!-- Generated by pkgdown: do not edit by hand --><html lang="en">
|
||||
<head>
|
||||
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
|
||||
<meta charset="utf-8">
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
|
||||
<meta name="description" content="REDCapCAST">
|
||||
<title>Shiny-app • REDCapCAST</title>
|
||||
<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
|
||||
<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
|
||||
<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
|
||||
<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
|
||||
<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous">
|
||||
<!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Shiny-app">
|
||||
<meta property="og:description" content="REDCapCAST">
|
||||
<meta property="og:image" content="https://agdamsbo.github.io/REDCapCAST/logo.png">
|
||||
<!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
|
||||
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
|
||||
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
|
||||
<![endif]-->
|
||||
</head>
|
||||
<body>
|
||||
<a href="#main" class="visually-hidden-focusable">Skip to contents</a>
|
||||
|
||||
|
||||
<nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">REDCapCAST</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">24.2.1</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
<span class="navbar-toggler-icon"></span>
|
||||
</button>
|
||||
|
||||
<div id="navbar" class="collapse navbar-collapse ms-3">
|
||||
<ul class="navbar-nav me-auto">
|
||||
<li class="nav-item">
|
||||
<a class="nav-link" href="../reference/index.html">Reference</a>
|
||||
</li>
|
||||
<li class="active 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>
|
||||
<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/Shiny-app.html">Shiny-app</a>
|
||||
</div>
|
||||
</li>
|
||||
<li class="nav-item">
|
||||
<a class="nav-link" href="../news/index.html">Changelog</a>
|
||||
</li>
|
||||
</ul>
|
||||
<form class="form-inline my-2 my-lg-0" role="search">
|
||||
<input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off">
|
||||
</form>
|
||||
|
||||
<ul class="navbar-nav">
|
||||
<li class="nav-item">
|
||||
<a class="external-link nav-link" href="https://github.com/agdamsbo/REDCapCAST/" aria-label="github">
|
||||
<span class="fab fa fab fa-github fa-lg"></span>
|
||||
|
||||
</a>
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
</nav><div class="container template-article">
|
||||
|
||||
|
||||
|
||||
|
||||
<div class="row">
|
||||
<main id="main" class="col-md-9"><div class="page-header">
|
||||
<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>
|
||||
</main>
|
||||
</div>
|
||||
|
||||
|
||||
|
||||
<footer><div class="pkgdown-footer-left">
|
||||
<p></p>
|
||||
<p>Developed by Andreas Gammelgaard Damsbo, Paul Egeler.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown-footer-right">
|
||||
<p></p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
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||||
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||||
</footer>
|
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|
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||||
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|
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</body>
|
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</html>
|
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@ -24,7 +24,9 @@
|
||||
<li class="nav-item dropdown">
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<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
|
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<a class="dropdown-item" href="../articles/Database-creation.html">Database-creation</a>
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|
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<a class="dropdown-item" href="../articles/Shiny-app.html">Shiny-app</a>
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|
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@ -53,7 +55,11 @@
|
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<h3>All vignettes</h3>
|
||||
<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>
|
||||
<dd>
|
||||
</dd><dt><a href="Introduction.html">Introduction</a></dt>
|
||||
<dd>
|
||||
</dd><dt><a href="Shiny-app.html">Shiny-app</a></dt>
|
||||
<dd>
|
||||
</dd></dl></div>
|
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</main></div>
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@ -24,7 +24,9 @@
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<li class="nav-item dropdown">
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<a class="dropdown-item" href="articles/Database-creation.html">Database-creation</a>
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<a class="dropdown-item" href="articles/Shiny-app.html">Shiny-app</a>
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<li class="nav-item">
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31
index.html
31
index.html
@ -7,10 +7,9 @@
|
||||
<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.
|
||||
See <https://github.com/pegeler/REDCapRITS>.
|
||||
Handles castellated datasets from REDCap projects with repeating instruments.
|
||||
Assists in casting tidy tables from raw REDCap data exports for each
|
||||
repeated instrument. Keeps a focused data export approach, by allowing to
|
||||
only export required data from the database.
|
||||
REDCap database casting and handling of castellated data when using
|
||||
repeated instruments and longitudinal projects. Keeps a focused data export
|
||||
approach, by allowing to only export required data from the database.
|
||||
REDCap (Research Electronic Data Capture) is a secure, web-based software
|
||||
platform designed to support data capture for research studies, providing
|
||||
1) an intuitive interface for validated data capture; 2) audit trails for
|
||||
@ -33,10 +32,9 @@
|
||||
<!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="pkgdown.js"></script><meta property="og:title" content="REDCap Castellated Data Handling">
|
||||
<meta property="og:description" content="Originally forked from the R part of REDCapRITS by Paul Egeler.
|
||||
See <https://github.com/pegeler/REDCapRITS>.
|
||||
Handles castellated datasets from REDCap projects with repeating instruments.
|
||||
Assists in casting tidy tables from raw REDCap data exports for each
|
||||
repeated instrument. Keeps a focused data export approach, by allowing to
|
||||
only export required data from the database.
|
||||
REDCap database casting and handling of castellated data when using
|
||||
repeated instruments and longitudinal projects. Keeps a focused data export
|
||||
approach, by allowing to only export required data from the database.
|
||||
REDCap (Research Electronic Data Capture) is a secure, web-based software
|
||||
platform designed to support data capture for research studies, providing
|
||||
1) an intuitive interface for validated data capture; 2) audit trails for
|
||||
@ -74,7 +72,9 @@
|
||||
<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>
|
||||
<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/Shiny-app.html">Shiny-app</a>
|
||||
</div>
|
||||
</li>
|
||||
<li class="nav-item">
|
||||
@ -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>
|
||||
</h1>
|
||||
</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>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">
|
||||
<h2 id="use-and-immprovements">Use and immprovements<a class="anchor" aria-label="anchor" href="#use-and-immprovements"></a>
|
||||
</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>
|
||||
<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/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/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>: 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/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>
|
||||
<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 class="section level2">
|
||||
<h2 id="future">Future<a class="anchor" aria-label="anchor" href="#future"></a>
|
||||
</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 class="section level2">
|
||||
<h2 id="installation">Installation<a class="anchor" aria-label="anchor" href="#installation"></a>
|
||||
|
||||
@ -24,7 +24,9 @@
|
||||
<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>
|
||||
<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/Shiny-app.html">Shiny-app</a>
|
||||
</div>
|
||||
</li>
|
||||
<li class="active nav-item">
|
||||
|
||||
@ -2,8 +2,10 @@ pandoc: 2.19.2
|
||||
pkgdown: 2.0.7
|
||||
pkgdown_sha: ~
|
||||
articles:
|
||||
Database-creation: Database-creation.html
|
||||
Introduction: Introduction.html
|
||||
last_built: 2024-02-26T20:10Z
|
||||
Shiny-app: Shiny-app.html
|
||||
last_built: 2024-02-27T11:56Z
|
||||
urls:
|
||||
reference: https://agdamsbo.github.io/REDCapCAST/reference
|
||||
article: https://agdamsbo.github.io/REDCapCAST/articles
|
||||
|
||||
@ -28,7 +28,9 @@ is used to determine which fields should be included in each resultant table."><
|
||||
<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>
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|
||||
<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/Shiny-app.html">Shiny-app</a>
|
||||
</div>
|
||||
</li>
|
||||
<li class="nav-item">
|
||||
|
||||
@ -28,7 +28,9 @@ Trying to make up for different naming conventions."><meta property="og:image" c
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||||
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|
||||
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
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|
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<a class="dropdown-item" href="../articles/Database-creation.html">Database-creation</a>
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<a class="dropdown-item" href="../articles/Introduction.html">Introduction</a>
|
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|
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|
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|
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<li class="nav-item">
|
||||
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@ -24,7 +24,9 @@
|
||||
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|
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<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
|
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<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>
|
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|
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|
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108
reference/deploy_shiny.html
Normal file
108
reference/deploy_shiny.html
Normal file
@ -0,0 +1,108 @@
|
||||
<!DOCTYPE html>
|
||||
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<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>
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|
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|
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<dd><p>app folder path</p></dd>
|
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<dt>name.app</dt>
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<p>deploy</p>
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<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># deploy_shiny</span></span></span>
|
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<span class="r-in"><span></span></span>
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<span class="r-in"></span>
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</code></pre></div>
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@ -30,7 +30,9 @@ has to be converted to character class before REDCap upload.'><meta property="og
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<dd>Convert single digits to words</dd>
|
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</dl><dl><dt>
|
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|
||||
<code><a href="deploy_shiny.html">deploy_shiny()</a></code>
|
||||
</dt>
|
||||
<dd>Deploy the Shiny app with rsconnect</dd>
|
||||
</dl><dl><dt>
|
||||
|
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<code><a href="ds2dd.html">ds2dd()</a></code>
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</dt>
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<dd>(DEPRECATED) Data set to data dictionary function</dd>
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@ -137,6 +144,11 @@
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<dd>Match fields to forms</dd>
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</dl><dl><dt>
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||||
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||||
<code><a href="mtcars_redcap.html">mtcars_redcap</a></code>
|
||||
</dt>
|
||||
<dd>mtcars dataset slightly modified to use for Shiny app upload demonstration</dd>
|
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</dl><dl><dt>
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||||
<code><a href="read_input.html">read_input()</a></code>
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<dd>Flexible file import based on extension</dd>
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129
reference/mtcars_redcap.html
Normal file
129
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|
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<!DOCTYPE html>
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<img src="../logo.png" class="logo" alt=""><h1>mtcars dataset slightly modified to use for Shiny app upload demonstration</h1>
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<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>
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<h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
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<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>
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<div class="section level2">
|
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<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>
|
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|
||||
<loc>https://agdamsbo.github.io/REDCapCAST/reference/deploy_shiny.html</loc>
|
||||
</url>
|
||||
<url>
|
||||
<loc>https://agdamsbo.github.io/REDCapCAST/reference/ds2dd.html</loc>
|
||||
</url>
|
||||
@ -69,6 +78,9 @@
|
||||
<url>
|
||||
<loc>https://agdamsbo.github.io/REDCapCAST/reference/match_fields_to_form.html</loc>
|
||||
</url>
|
||||
<url>
|
||||
<loc>https://agdamsbo.github.io/REDCapCAST/reference/mtcars_redcap.html</loc>
|
||||
</url>
|
||||
<url>
|
||||
<loc>https://agdamsbo.github.io/REDCapCAST/reference/read_input.html</loc>
|
||||
</url>
|
||||
|
||||
Loading…
Reference in New Issue
Block a user