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@ -74,14 +74,54 @@
<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>This vignette covers the included functions and basic
functionality.</p>
<p>A dataset and a meta data file are provided with the package for
demonstration of the functions.</p>
<p>This vignette covers the basics to get you started with the two basic
features of REDCapCAST:</p>
<ul>
<li><p>Casting REDCap metadata to create a new REDCap database or extend
an existing with a new instrument</p></li>
<li><p>Reading REDCap data in a convenient and focused way, by only
getting the data you need, while preserving as much metadata as
possible.</p></li>
</ul>
<div class="section level2">
<h2 id="casting-meta-data">Casting meta data<a class="anchor" aria-label="anchor" href="#casting-meta-data"></a>
</h2>
<p>The easiest way is to use the <code><a href="../reference/shiny_cast.html">shiny_cast()</a></code>. You can
access a <a href="https://agdamsbo.shinyapps.io/redcapcast/" class="external-link">hosted
version here</a> or launch it locally like this:</p>
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
<code class="sourceCode R"><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>
</div>
<div class="section level2">
<h2 id="reading-data-from-redcap">Reading data from REDCap<a class="anchor" aria-label="anchor" href="#reading-data-from-redcap"></a>
</h2>
<p>To get you started, the easiest way possible, you can use the
<code><a href="../reference/easy_redcap.html">easy_redcap()</a></code> function (example below).</p>
<p>You will need an API-key for your REDCap server, the uri/URL/address
for the API connection (usually “<a href="https://redcap.YOUR-institution.site/api/" class="external-link uri">https://redcap.YOUR-institution.site/api/</a>”).</p>
<p>This function includes a few convenience features to ease your
further work.</p>
<p>If your project uses repeating instruments possible as a longitudinal
project, you can choose to widen the data. If not, the result will be a
list of each instrument you have chosen to extract data from. Make sure
to specify only the fields or instruments you need, and avoid to save
any of the data locally, but always source from REDCap to avoid possibly
insecure local storage of sensitive data.</p>
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../reference/easy_redcap.html">easy_redcap</a></span><span class="op">(</span>uri <span class="op">=</span> <span class="st">"YOUR URI"</span>, </span>
<span> project.name <span class="op">=</span> <span class="st">"MY_PROJECT"</span>, </span>
<span> widen.data <span class="op">=</span> <span class="cn">TRUE</span>,</span>
<span> fields <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"record_id"</span>, <span class="st">"OTHER FIELDS"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
</div>
<div class="section level2">
<h2 id="splitting-the-dataset">Splitting the dataset<a class="anchor" aria-label="anchor" href="#splitting-the-dataset"></a>
</h2>
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
<p>The <code><a href="../reference/easy_redcap.html">easy_redcap()</a></code> function does a few things under the
hood. Below are a few examples to show how the nicely formatted output
is achieved.</p>
<p>A sample dataset and Data Dictionary/metadata is provided for this
demonstration:</p>
<div class="sourceCode" id="cb4"><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>
<div id="mwlefoodfi" style="padding-left:0px;padding-right:0px;padding-top:10px;padding-bottom:10px;overflow-x:auto;overflow-y:auto;width:auto;height:auto;">
<style>#mwlefoodfi table {
@ -1291,7 +1331,7 @@ demonstration of the functions.</p>
</tbody>
</table>
</div>
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb5"><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>
<div id="eexombwkke" style="padding-left:0px;padding-right:0px;padding-top:10px;padding-bottom:10px;overflow-x:auto;overflow-y:auto;width:auto;height:auto;">
<style>#eexombwkke table {
@ -2189,136 +2229,723 @@ Note: as opposed to the build in datediff() this handles counting years as integ
</tbody>
</table>
</div>
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
<p>To save the metadata as labels in the dataset, we can save field
labels and the choices from radio buttons and dropdown features:</p>
<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">labelled_data</span> <span class="op">&lt;-</span> </span>
<span> <span class="fu"><a href="../reference/apply_field_label.html">apply_field_label</a></span><span class="op">(</span>data<span class="op">=</span><span class="va">redcapcast_data</span>,</span>
<span> meta<span class="op">=</span><span class="va">redcapcast_meta</span><span class="op">)</span> <span class="op">|&gt;</span> </span>
<span> <span class="fu"><a href="../reference/apply_factor_labels.html">apply_factor_labels</a></span><span class="op">(</span>meta<span class="op">=</span><span class="va">redcapcast_meta</span><span class="op">)</span></span></code></pre></div>
<p>The <code>REDCap_split</code> function splits the data set into a
list of data.frames.</p>
<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">list</span> <span class="op">&lt;-</span></span>
<span> <span class="fu"><a href="../reference/REDCap_split.html">REDCap_split</a></span><span class="op">(</span></span>
<span> records <span class="op">=</span> <span class="va">redcapcast_data</span>,</span>
<span> records <span class="op">=</span> <span class="va">labelled_data</span>,</span>
<span> metadata <span class="op">=</span> <span class="va">redcapcast_meta</span>,</span>
<span> forms <span class="op">=</span> <span class="st">"all"</span></span>
<span> <span class="op">)</span> <span class="op">|&gt;</span> </span>
<span> <span class="co"># Next steps cleans up and removes generic columns</span></span>
<span> <span class="fu"><a href="../reference/sanitize_split.html">sanitize_split</a></span><span class="op">(</span><span class="op">)</span></span>
<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="va">list</span><span class="op">)</span></span>
<span><span class="co">#&gt; List of 4</span></span>
<span><span class="co">#&gt; List of 3</span></span>
<span><span class="co">#&gt; $ baseline_data_start: tibble [6 × 14] (S3: tbl_df/tbl/data.frame)</span></span>
<span><span class="co">#&gt; ..$ record_id : num [1:6] 1 2 3 4 5 6</span></span>
<span><span class="co">#&gt; .. ..- attr(*, "label")= chr "ID"</span></span>
<span><span class="co">#&gt; ..$ redcap_event_name : chr [1:6] "inclusion" "inclusion" "inclusion" "inclusion" ...</span></span>
<span><span class="co">#&gt; ..$ cpr : chr [1:6] "1203401OB4" "0102342303" "2301569823" "0204051342" ...</span></span>
<span><span class="co">#&gt; .. ..- attr(*, "label")= chr "CPR (Danish civil registration number)"</span></span>
<span><span class="co">#&gt; ..$ inclusion : Date[1:6], format: "2023-03-13" "2023-03-01" ...</span></span>
<span><span class="co">#&gt; ..$ inclusion_time : 'hms' num [1:6] 12:38:49 10:38:57 12:01:07 20:39:19 ...</span></span>
<span><span class="co">#&gt; .. ..- attr(*, "units")= chr "secs"</span></span>
<span><span class="co">#&gt; ..$ dob : Date[1:6], format: "1940-03-12" "1934-02-01" ...</span></span>
<span><span class="co">#&gt; ..$ age : num [1:6] 83 89.1 66.1 117.9 126.2 ...</span></span>
<span><span class="co">#&gt; .. ..- attr(*, "label")= chr "Age\r\nNote: Apparently, the build in datediff() function does not handle counting whole years. This results in"| __truncated__</span></span>
<span><span class="co">#&gt; ..$ age_integer : num [1:6] 83 89 66 117 126 91</span></span>
<span><span class="co">#&gt; .. ..- attr(*, "label")= chr "Age integer\r\nNote: as opposed to the build in datediff() this handles counting years as integers very well. C"| __truncated__</span></span>
<span><span class="co">#&gt; ..$ sex : chr [1:6] "female" "male" "male" "female" ...</span></span>
<span><span class="co">#&gt; ..$ cohabitation : chr [1:6] "Yes" "Yes" "No" NA ...</span></span>
<span><span class="co">#&gt; ..$ hypertension : chr [1:6] "No" "No" "Yes" NA ...</span></span>
<span><span class="co">#&gt; ..$ diabetes : chr [1:6] "Yes" "No" "Yes" NA ...</span></span>
<span><span class="co">#&gt; ..$ region : chr [1:6] "East" "South" "North" NA ...</span></span>
<span><span class="co">#&gt; .. ..- attr(*, "label")= chr "Legal sex"</span></span>
<span><span class="co">#&gt; ..$ cohabitation : 'labelled' chr [1:6] "Yes" "Yes" "No" NA ...</span></span>
<span><span class="co">#&gt; .. ..- attr(*, "label")= chr "Cohabitation"</span></span>
<span><span class="co">#&gt; .. ..- attr(*, "labels")= Named chr [1:2] "1" "2"</span></span>
<span><span class="co">#&gt; .. .. ..- attr(*, "names")= chr [1:2] "Yes" "No"</span></span>
<span><span class="co">#&gt; ..$ hypertension : 'labelled' chr [1:6] "No" "No" "Yes" NA ...</span></span>
<span><span class="co">#&gt; .. ..- attr(*, "label")= chr "Hypertension"</span></span>
<span><span class="co">#&gt; .. ..- attr(*, "labels")= Named chr [1:2] "1" "2"</span></span>
<span><span class="co">#&gt; .. .. ..- attr(*, "names")= chr [1:2] "Yes" "No"</span></span>
<span><span class="co">#&gt; ..$ diabetes : 'labelled' chr [1:6] "Yes" "No" "Yes" NA ...</span></span>
<span><span class="co">#&gt; .. ..- attr(*, "label")= chr "Diabetes"</span></span>
<span><span class="co">#&gt; .. ..- attr(*, "labels")= Named chr [1:2] "1" "2"</span></span>
<span><span class="co">#&gt; .. .. ..- attr(*, "names")= chr [1:2] "Yes" "No"</span></span>
<span><span class="co">#&gt; ..$ region : 'labelled' chr [1:6] "East" "South" "North" NA ...</span></span>
<span><span class="co">#&gt; .. ..- attr(*, "label")= chr "Region"</span></span>
<span><span class="co">#&gt; .. ..- attr(*, "labels")= Named chr [1:4] "1" "2" "3" "4"</span></span>
<span><span class="co">#&gt; .. .. ..- attr(*, "names")= chr [1:4] "North" "East" "South" "West"</span></span>
<span><span class="co">#&gt; ..$ baseline_data_start_complete: chr [1:6] "Incomplete" "Incomplete" "Incomplete" "Incomplete" ...</span></span>
<span><span class="co">#&gt; ..- attr(*, "problems")=&lt;externalptr&gt; </span></span>
<span><span class="co">#&gt; $ mrs : tibble [5 × 6] (S3: tbl_df/tbl/data.frame)</span></span>
<span><span class="co">#&gt; ..$ record_id : num [1:5] 1 2 2 3 3</span></span>
<span><span class="co">#&gt; .. ..- attr(*, "label")= chr "ID"</span></span>
<span><span class="co">#&gt; ..$ redcap_event_name: chr [1:5] "inclusion" "inclusion" "follow1" "follow1" ...</span></span>
<span><span class="co">#&gt; ..$ mrs_assessed : chr [1:5] "Yes" "Yes" "Yes" "Yes" ...</span></span>
<span><span class="co">#&gt; ..$ mrs_assessed : 'labelled' chr [1:5] "Yes" "Yes" "Yes" "Yes" ...</span></span>
<span><span class="co">#&gt; .. ..- attr(*, "label")= chr "Assesed"</span></span>
<span><span class="co">#&gt; .. ..- attr(*, "labels")= Named chr [1:2] "1" "2"</span></span>
<span><span class="co">#&gt; .. .. ..- attr(*, "names")= chr [1:2] "Yes" "No"</span></span>
<span><span class="co">#&gt; ..$ mrs_date : Date[1:5], format: "2023-03-13" "2023-03-07" ...</span></span>
<span><span class="co">#&gt; ..$ mrs_score : num [1:5] 1 1 3 2 1</span></span>
<span><span class="co">#&gt; ..$ mrs_score : 'labelled' num [1:5] 1 1 3 2 1</span></span>
<span><span class="co">#&gt; .. ..- attr(*, "label")= chr "mRS score"</span></span>
<span><span class="co">#&gt; .. ..- attr(*, "labels")= Named chr [1:6] "0" "1" "2" "3" ...</span></span>
<span><span class="co">#&gt; .. .. ..- attr(*, "names")= chr [1:6] "0" "1" "2" "3" ...</span></span>
<span><span class="co">#&gt; ..$ mrs_complete : chr [1:5] "Incomplete" "Incomplete" "Incomplete" "Incomplete" ...</span></span>
<span><span class="co">#&gt; ..- attr(*, "problems")=&lt;externalptr&gt; </span></span>
<span><span class="co">#&gt; $ consensus : tibble [0 × 5] (S3: tbl_df/tbl/data.frame)</span></span>
<span><span class="co">#&gt; ..$ record_id : num(0) </span></span>
<span><span class="co">#&gt; ..$ redcap_event_name : chr(0) </span></span>
<span><span class="co">#&gt; ..$ con_mrs : logi(0) </span></span>
<span><span class="co">#&gt; ..$ con_calc : logi(0) </span></span>
<span><span class="co">#&gt; ..$ consensus_complete: chr(0) </span></span>
<span><span class="co">#&gt; ..- attr(*, "problems")=&lt;externalptr&gt; </span></span>
<span><span class="co">#&gt; $ new_event : tibble [13 × 8] (S3: tbl_df/tbl/data.frame)</span></span>
<span><span class="co">#&gt; ..$ record_id : num [1:13] 2 3 3 3 3 3 4 4 4 4 ...</span></span>
<span><span class="co">#&gt; .. ..- attr(*, "label")= chr "ID"</span></span>
<span><span class="co">#&gt; ..$ redcap_event_name : chr [1:13] "follow1" "follow1" "follow1" "follow2" ...</span></span>
<span><span class="co">#&gt; ..$ redcap_repeat_instrument: chr [1:13] "new_event" "new_event" "new_event" "new_event" ...</span></span>
<span><span class="co">#&gt; ..$ redcap_repeat_instance : num [1:13] 1 1 2 1 2 3 1 2 1 2 ...</span></span>
<span><span class="co">#&gt; ..$ event_datetime : POSIXct[1:13], format: "2024-01-18 12:49:42" "2024-01-18 12:49:58" ...</span></span>
<span><span class="co">#&gt; ..$ event_age : num [1:13] NA NA NA NA NA NA 96 105 118 118 ...</span></span>
<span><span class="co">#&gt; ..$ event_type : chr [1:13] "TIA" "AIS" "ICH" "ICH" ...</span></span>
<span><span class="co">#&gt; ..$ new_event_complete : chr [1:13] "Incomplete" "Incomplete" "Incomplete" "Incomplete" ...</span></span>
<span><span class="co">#&gt; ..- attr(*, "problems")=&lt;externalptr&gt;</span></span></code></pre></div>
</div>
<div class="section level2">
<h2 id="reading-data-from-redcap">Reading data from REDCap<a class="anchor" aria-label="anchor" href="#reading-data-from-redcap"></a>
</h2>
<p>This function wraps all the above demonstrated function to get the
dataset, the metadata, apply the <code>REDCap_split</code>function and
then a bit of cleaning. It just cuts outs all the steps for an easier
approach.</p>
<p>The function works very similar to the
<code><a href="https://ouhscbbmc.github.io/REDCapR/reference/redcap_read.html" class="external-link">REDCapR::redcap_read()</a></code> in allowing to specify fields,
events and forms for export instead of exporting the whole database and
filtering afterwards. I believe this is a better and safer, focused
approach.</p>
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># read_redcap_tables(uri = "YOUR URI", token = "YOUR TOKEN")</span></span></code></pre></div>
</div>
<div class="section level2">
<h2 id="pivotting-to-wider-format">Pivotting to wider format<a class="anchor" aria-label="anchor" href="#pivotting-to-wider-format"></a>
</h2>
<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../reference/redcap_wider.html">redcap_wider</a></span><span class="op">(</span><span class="va">list</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>
<span><span class="co">#&gt; .. ..- attr(*, "label")= chr "Age at event"</span></span>
<span><span class="co">#&gt; ..$ event_type : 'labelled' chr [1:13] "TIA" "AIS" "ICH" "ICH" ...</span></span>
<span><span class="co">#&gt; .. ..- attr(*, "label")= chr "Neurovascular event"</span></span>
<span><span class="co">#&gt; .. ..- attr(*, "labels")= Named chr [1:5] "1" "2" "3" "4" ...</span></span>
<span><span class="co">#&gt; .. .. ..- attr(*, "names")= chr [1:5] "TIA" "AIS" "ICH" "SAH" ...</span></span>
<span><span class="co">#&gt; ..$ new_event_complete : chr [1:13] "Incomplete" "Incomplete" "Incomplete" "Incomplete" ...</span></span></code></pre></div>
<p>The <code><a href="../reference/easy_redcap.html">easy_redcap()</a></code> will then (optionally) continue to
widen the data, by transforming the list of data.frames to a single
data.frame with one row for each subject/record_id (wide data
format):</p>
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">wide_data</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/redcap_wider.html">redcap_wider</a></span><span class="op">(</span><span class="va">list</span><span class="op">)</span> </span>
<span><span class="co">#&gt; Joining with `by = join_by(record_id)`</span></span>
<span><span class="co">#&gt; Joining with `by = join_by(record_id)`</span></span>
<span><span class="co">#&gt; Joining with `by = join_by(record_id)`</span></span>
<span><span class="co">#&gt; 'data.frame': 6 obs. of 52 variables:</span></span>
<span><span class="co">#&gt; $ record_id : num 1 2 3 4 5 6</span></span>
<span><span class="co">#&gt; $ cpr : chr "1203401OB4" "0102342303" "2301569823" "0204051342" ...</span></span>
<span><span class="co">#&gt; $ inclusion : Date, format: "2023-03-13" "2023-03-01" ...</span></span>
<span><span class="co">#&gt; $ inclusion_time : 'hms' num 12:38:49 10:38:57 12:01:07 20:39:19 ...</span></span>
<span><span class="va">wide_data</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>
<span><span class="co">#&gt; tibble [6 × 49] (S3: tbl_df/tbl/data.frame)</span></span>
<span><span class="co">#&gt; $ record_id : num [1:6] 1 2 3 4 5 6</span></span>
<span><span class="co">#&gt; ..- attr(*, "label")= chr "ID"</span></span>
<span><span class="co">#&gt; $ cpr : chr [1:6] "1203401OB4" "0102342303" "2301569823" "0204051342" ...</span></span>
<span><span class="co">#&gt; ..- attr(*, "label")= chr "CPR (Danish civil registration number)"</span></span>
<span><span class="co">#&gt; $ inclusion : Date[1:6], format: "2023-03-13" "2023-03-01" ...</span></span>
<span><span class="co">#&gt; $ inclusion_time : 'hms' num [1:6] 12:38:49 10:38:57 12:01:07 20:39:19 ...</span></span>
<span><span class="co">#&gt; ..- attr(*, "units")= chr "secs"</span></span>
<span><span class="co">#&gt; $ dob : Date, format: "1940-03-12" "1934-02-01" ...</span></span>
<span><span class="co">#&gt; $ age : num 83 89.1 66.1 117.9 126.2 ...</span></span>
<span><span class="co">#&gt; $ age_integer : num 83 89 66 117 126 91</span></span>
<span><span class="co">#&gt; $ sex : chr "female" "male" "male" "female" ...</span></span>
<span><span class="co">#&gt; $ cohabitation : chr "Yes" "Yes" "No" NA ...</span></span>
<span><span class="co">#&gt; $ hypertension : chr "No" "No" "Yes" NA ...</span></span>
<span><span class="co">#&gt; $ diabetes : chr "Yes" "No" "Yes" NA ...</span></span>
<span><span class="co">#&gt; $ region : chr "East" "South" "North" NA ...</span></span>
<span><span class="co">#&gt; $ baseline_data_start_complete: chr "Incomplete" "Incomplete" "Incomplete" "Incomplete" ...</span></span>
<span><span class="co">#&gt; $ mrs_assessed_inclusion : chr "Yes" "Yes" NA NA ...</span></span>
<span><span class="co">#&gt; $ mrs_assessed_follow1 : chr NA "Yes" "Yes" NA ...</span></span>
<span><span class="co">#&gt; $ mrs_assessed_follow2 : chr NA NA "Yes" NA ...</span></span>
<span><span class="co">#&gt; $ mrs_date_inclusion : Date, format: "2023-03-13" "2023-03-07" ...</span></span>
<span><span class="co">#&gt; $ mrs_date_follow1 : Date, format: NA "2023-03-09" ...</span></span>
<span><span class="co">#&gt; $ mrs_date_follow2 : Date, format: NA NA ...</span></span>
<span><span class="co">#&gt; $ mrs_score_inclusion : num 1 1 NA NA NA NA</span></span>
<span><span class="co">#&gt; $ mrs_score_follow1 : num NA 3 2 NA NA NA</span></span>
<span><span class="co">#&gt; $ mrs_score_follow2 : num NA NA 1 NA NA NA</span></span>
<span><span class="co">#&gt; $ mrs_complete_inclusion : chr "Incomplete" "Incomplete" NA NA ...</span></span>
<span><span class="co">#&gt; $ mrs_complete_follow1 : chr NA "Incomplete" "Incomplete" NA ...</span></span>
<span><span class="co">#&gt; $ mrs_complete_follow2 : chr NA NA "Incomplete" NA ...</span></span>
<span><span class="co">#&gt; $ con_mrs : logi NA NA NA NA NA NA</span></span>
<span><span class="co">#&gt; $ con_calc : logi NA NA NA NA NA NA</span></span>
<span><span class="co">#&gt; $ consensus_complete : chr NA NA NA NA ...</span></span>
<span><span class="co">#&gt; $ event_datetime_1_follow1 : POSIXct, format: NA "2024-01-18 12:49:42" ...</span></span>
<span><span class="co">#&gt; $ event_datetime_1_follow2 : POSIXct, format: NA NA ...</span></span>
<span><span class="co">#&gt; $ event_age_1_follow1 : num NA NA NA 96 127 NA</span></span>
<span><span class="co">#&gt; $ event_age_1_follow2 : num NA NA NA 118 NA NA</span></span>
<span><span class="co">#&gt; $ event_type_1_follow1 : chr NA "TIA" "AIS" "TIA" ...</span></span>
<span><span class="co">#&gt; $ event_type_1_follow2 : chr NA NA "ICH" "AIS" ...</span></span>
<span><span class="co">#&gt; $ new_event_complete_1_follow1: chr NA "Incomplete" "Incomplete" "Complete" ...</span></span>
<span><span class="co">#&gt; $ new_event_complete_1_follow2: chr NA NA "Incomplete" "Complete" ...</span></span>
<span><span class="co">#&gt; $ event_datetime_2_follow1 : POSIXct, format: NA NA ...</span></span>
<span><span class="co">#&gt; $ event_datetime_2_follow2 : POSIXct, format: NA NA ...</span></span>
<span><span class="co">#&gt; $ event_datetime_3_follow1 : POSIXct, format: NA NA ...</span></span>
<span><span class="co">#&gt; $ event_datetime_3_follow2 : POSIXct, format: NA NA ...</span></span>
<span><span class="co">#&gt; $ event_age_2_follow1 : num NA NA NA 105 127 NA</span></span>
<span><span class="co">#&gt; $ event_age_2_follow2 : num NA NA NA 118 NA NA</span></span>
<span><span class="co">#&gt; $ event_age_3_follow1 : num NA NA NA NA NA NA</span></span>
<span><span class="co">#&gt; $ event_age_3_follow2 : num NA NA NA 118 NA NA</span></span>
<span><span class="co">#&gt; $ event_type_2_follow1 : chr NA NA "ICH" "TIA" ...</span></span>
<span><span class="co">#&gt; $ event_type_2_follow2 : chr NA NA "TIA" "ICH" ...</span></span>
<span><span class="co">#&gt; $ event_type_3_follow1 : chr NA NA NA NA ...</span></span>
<span><span class="co">#&gt; $ event_type_3_follow2 : chr NA NA "AIS" "Unknown" ...</span></span>
<span><span class="co">#&gt; $ new_event_complete_2_follow1: chr NA NA "Incomplete" "Complete" ...</span></span>
<span><span class="co">#&gt; $ new_event_complete_2_follow2: chr NA NA "Incomplete" "Incomplete" ...</span></span>
<span><span class="co">#&gt; $ new_event_complete_3_follow1: chr NA NA NA NA ...</span></span>
<span><span class="co">#&gt; $ new_event_complete_3_follow2: chr NA NA "Incomplete" "Complete" ...</span></span></code></pre></div>
<span><span class="co">#&gt; $ dob : Date[1:6], format: "1940-03-12" "1934-02-01" ...</span></span>
<span><span class="co">#&gt; $ age : num [1:6] 83 89.1 66.1 117.9 126.2 ...</span></span>
<span><span class="co">#&gt; ..- attr(*, "label")= chr "Age\r\nNote: Apparently, the build in datediff() function does not handle counting whole years. This results in"| __truncated__</span></span>
<span><span class="co">#&gt; $ age_integer : num [1:6] 83 89 66 117 126 91</span></span>
<span><span class="co">#&gt; ..- attr(*, "label")= chr "Age integer\r\nNote: as opposed to the build in datediff() this handles counting years as integers very well. C"| __truncated__</span></span>
<span><span class="co">#&gt; $ sex : chr [1:6] "female" "male" "male" "female" ...</span></span>
<span><span class="co">#&gt; ..- attr(*, "label")= chr "Legal sex"</span></span>
<span><span class="co">#&gt; $ cohabitation : 'labelled' chr [1:6] "Yes" "Yes" "No" NA ...</span></span>
<span><span class="co">#&gt; ..- attr(*, "label")= chr "Cohabitation"</span></span>
<span><span class="co">#&gt; ..- attr(*, "labels")= Named chr [1:2] "1" "2"</span></span>
<span><span class="co">#&gt; .. ..- attr(*, "names")= chr [1:2] "Yes" "No"</span></span>
<span><span class="co">#&gt; $ hypertension : 'labelled' chr [1:6] "No" "No" "Yes" NA ...</span></span>
<span><span class="co">#&gt; ..- attr(*, "label")= chr "Hypertension"</span></span>
<span><span class="co">#&gt; ..- attr(*, "labels")= Named chr [1:2] "1" "2"</span></span>
<span><span class="co">#&gt; .. ..- attr(*, "names")= chr [1:2] "Yes" "No"</span></span>
<span><span class="co">#&gt; $ diabetes : 'labelled' chr [1:6] "Yes" "No" "Yes" NA ...</span></span>
<span><span class="co">#&gt; ..- attr(*, "label")= chr "Diabetes"</span></span>
<span><span class="co">#&gt; ..- attr(*, "labels")= Named chr [1:2] "1" "2"</span></span>
<span><span class="co">#&gt; .. ..- attr(*, "names")= chr [1:2] "Yes" "No"</span></span>
<span><span class="co">#&gt; $ region : 'labelled' chr [1:6] "East" "South" "North" NA ...</span></span>
<span><span class="co">#&gt; ..- attr(*, "label")= chr "Region"</span></span>
<span><span class="co">#&gt; ..- attr(*, "labels")= Named chr [1:4] "1" "2" "3" "4"</span></span>
<span><span class="co">#&gt; .. ..- attr(*, "names")= chr [1:4] "North" "East" "South" "West"</span></span>
<span><span class="co">#&gt; $ baseline_data_start_complete: chr [1:6] "Incomplete" "Incomplete" "Incomplete" "Incomplete" ...</span></span>
<span><span class="co">#&gt; $ mrs_assessed_inclusion : 'labelled' chr [1:6] "Yes" "Yes" NA NA ...</span></span>
<span><span class="co">#&gt; ..- attr(*, "label")= chr "Assesed"</span></span>
<span><span class="co">#&gt; ..- attr(*, "labels")= Named chr [1:2] "1" "2"</span></span>
<span><span class="co">#&gt; .. ..- attr(*, "names")= chr [1:2] "Yes" "No"</span></span>
<span><span class="co">#&gt; $ mrs_assessed_follow1 : 'labelled' chr [1:6] NA "Yes" "Yes" NA ...</span></span>
<span><span class="co">#&gt; ..- attr(*, "label")= chr "Assesed"</span></span>
<span><span class="co">#&gt; ..- attr(*, "labels")= Named chr [1:2] "1" "2"</span></span>
<span><span class="co">#&gt; .. ..- attr(*, "names")= chr [1:2] "Yes" "No"</span></span>
<span><span class="co">#&gt; $ mrs_assessed_follow2 : 'labelled' chr [1:6] NA NA "Yes" NA ...</span></span>
<span><span class="co">#&gt; ..- attr(*, "label")= chr "Assesed"</span></span>
<span><span class="co">#&gt; ..- attr(*, "labels")= Named chr [1:2] "1" "2"</span></span>
<span><span class="co">#&gt; .. ..- attr(*, "names")= chr [1:2] "Yes" "No"</span></span>
<span><span class="co">#&gt; $ mrs_date_inclusion : Date[1:6], format: "2023-03-13" "2023-03-07" ...</span></span>
<span><span class="co">#&gt; $ mrs_date_follow1 : Date[1:6], format: NA "2023-03-09" ...</span></span>
<span><span class="co">#&gt; $ mrs_date_follow2 : Date[1:6], format: NA NA ...</span></span>
<span><span class="co">#&gt; $ mrs_score_inclusion : 'labelled' num [1:6] 1 1 NA NA NA NA</span></span>
<span><span class="co">#&gt; ..- attr(*, "label")= chr "mRS score"</span></span>
<span><span class="co">#&gt; ..- attr(*, "labels")= Named chr [1:6] "0" "1" "2" "3" ...</span></span>
<span><span class="co">#&gt; .. ..- attr(*, "names")= chr [1:6] "0" "1" "2" "3" ...</span></span>
<span><span class="co">#&gt; $ mrs_score_follow1 : 'labelled' num [1:6] NA 3 2 NA NA NA</span></span>
<span><span class="co">#&gt; ..- attr(*, "label")= chr "mRS score"</span></span>
<span><span class="co">#&gt; ..- attr(*, "labels")= Named chr [1:6] "0" "1" "2" "3" ...</span></span>
<span><span class="co">#&gt; .. ..- attr(*, "names")= chr [1:6] "0" "1" "2" "3" ...</span></span>
<span><span class="co">#&gt; $ mrs_score_follow2 : 'labelled' num [1:6] NA NA 1 NA NA NA</span></span>
<span><span class="co">#&gt; ..- attr(*, "label")= chr "mRS score"</span></span>
<span><span class="co">#&gt; ..- attr(*, "labels")= Named chr [1:6] "0" "1" "2" "3" ...</span></span>
<span><span class="co">#&gt; .. ..- attr(*, "names")= chr [1:6] "0" "1" "2" "3" ...</span></span>
<span><span class="co">#&gt; $ mrs_complete_inclusion : chr [1:6] "Incomplete" "Incomplete" NA NA ...</span></span>
<span><span class="co">#&gt; $ mrs_complete_follow1 : chr [1:6] NA "Incomplete" "Incomplete" NA ...</span></span>
<span><span class="co">#&gt; $ mrs_complete_follow2 : chr [1:6] NA NA "Incomplete" NA ...</span></span>
<span><span class="co">#&gt; $ event_datetime_1_follow1 : POSIXct[1:6], format: NA "2024-01-18 12:49:42" ...</span></span>
<span><span class="co">#&gt; $ event_datetime_1_follow2 : POSIXct[1:6], format: NA NA ...</span></span>
<span><span class="co">#&gt; $ event_age_1_follow1 : num [1:6] NA NA NA 96 127 NA</span></span>
<span><span class="co">#&gt; ..- attr(*, "label")= chr "Age at event"</span></span>
<span><span class="co">#&gt; $ event_age_1_follow2 : num [1:6] NA NA NA 118 NA NA</span></span>
<span><span class="co">#&gt; ..- attr(*, "label")= chr "Age at event"</span></span>
<span><span class="co">#&gt; $ event_type_1_follow1 : 'labelled' chr [1:6] NA "TIA" "AIS" "TIA" ...</span></span>
<span><span class="co">#&gt; ..- attr(*, "label")= chr "Neurovascular event"</span></span>
<span><span class="co">#&gt; ..- attr(*, "labels")= Named chr [1:5] "1" "2" "3" "4" ...</span></span>
<span><span class="co">#&gt; .. ..- attr(*, "names")= chr [1:5] "TIA" "AIS" "ICH" "SAH" ...</span></span>
<span><span class="co">#&gt; $ event_type_1_follow2 : 'labelled' chr [1:6] NA NA "ICH" "AIS" ...</span></span>
<span><span class="co">#&gt; ..- attr(*, "label")= chr "Neurovascular event"</span></span>
<span><span class="co">#&gt; ..- attr(*, "labels")= Named chr [1:5] "1" "2" "3" "4" ...</span></span>
<span><span class="co">#&gt; .. ..- attr(*, "names")= chr [1:5] "TIA" "AIS" "ICH" "SAH" ...</span></span>
<span><span class="co">#&gt; $ new_event_complete_1_follow1: chr [1:6] NA "Incomplete" "Incomplete" "Complete" ...</span></span>
<span><span class="co">#&gt; $ new_event_complete_1_follow2: chr [1:6] NA NA "Incomplete" "Complete" ...</span></span>
<span><span class="co">#&gt; $ event_datetime_2_follow1 : POSIXct[1:6], format: NA NA ...</span></span>
<span><span class="co">#&gt; $ event_datetime_2_follow2 : POSIXct[1:6], format: NA NA ...</span></span>
<span><span class="co">#&gt; $ event_datetime_3_follow1 : POSIXct[1:6], format: NA NA ...</span></span>
<span><span class="co">#&gt; $ event_datetime_3_follow2 : POSIXct[1:6], format: NA NA ...</span></span>
<span><span class="co">#&gt; $ event_age_2_follow1 : num [1:6] NA NA NA 105 127 NA</span></span>
<span><span class="co">#&gt; ..- attr(*, "label")= chr "Age at event"</span></span>
<span><span class="co">#&gt; $ event_age_2_follow2 : num [1:6] NA NA NA 118 NA NA</span></span>
<span><span class="co">#&gt; ..- attr(*, "label")= chr "Age at event"</span></span>
<span><span class="co">#&gt; $ event_age_3_follow1 : num [1:6] NA NA NA NA NA NA</span></span>
<span><span class="co">#&gt; ..- attr(*, "label")= chr "Age at event"</span></span>
<span><span class="co">#&gt; $ event_age_3_follow2 : num [1:6] NA NA NA 118 NA NA</span></span>
<span><span class="co">#&gt; ..- attr(*, "label")= chr "Age at event"</span></span>
<span><span class="co">#&gt; $ event_type_2_follow1 : 'labelled' chr [1:6] NA NA "ICH" "TIA" ...</span></span>
<span><span class="co">#&gt; ..- attr(*, "label")= chr "Neurovascular event"</span></span>
<span><span class="co">#&gt; ..- attr(*, "labels")= Named chr [1:5] "1" "2" "3" "4" ...</span></span>
<span><span class="co">#&gt; .. ..- attr(*, "names")= chr [1:5] "TIA" "AIS" "ICH" "SAH" ...</span></span>
<span><span class="co">#&gt; $ event_type_2_follow2 : 'labelled' chr [1:6] NA NA "TIA" "ICH" ...</span></span>
<span><span class="co">#&gt; ..- attr(*, "label")= chr "Neurovascular event"</span></span>
<span><span class="co">#&gt; ..- attr(*, "labels")= Named chr [1:5] "1" "2" "3" "4" ...</span></span>
<span><span class="co">#&gt; .. ..- attr(*, "names")= chr [1:5] "TIA" "AIS" "ICH" "SAH" ...</span></span>
<span><span class="co">#&gt; $ event_type_3_follow1 : 'labelled' chr [1:6] NA NA NA NA ...</span></span>
<span><span class="co">#&gt; ..- attr(*, "label")= chr "Neurovascular event"</span></span>
<span><span class="co">#&gt; ..- attr(*, "labels")= Named chr [1:5] "1" "2" "3" "4" ...</span></span>
<span><span class="co">#&gt; .. ..- attr(*, "names")= chr [1:5] "TIA" "AIS" "ICH" "SAH" ...</span></span>
<span><span class="co">#&gt; $ event_type_3_follow2 : 'labelled' chr [1:6] NA NA "AIS" "Unknown" ...</span></span>
<span><span class="co">#&gt; ..- attr(*, "label")= chr "Neurovascular event"</span></span>
<span><span class="co">#&gt; ..- attr(*, "labels")= Named chr [1:5] "1" "2" "3" "4" ...</span></span>
<span><span class="co">#&gt; .. ..- attr(*, "names")= chr [1:5] "TIA" "AIS" "ICH" "SAH" ...</span></span>
<span><span class="co">#&gt; $ new_event_complete_2_follow1: chr [1:6] NA NA "Incomplete" "Complete" ...</span></span>
<span><span class="co">#&gt; $ new_event_complete_2_follow2: chr [1:6] NA NA "Incomplete" "Incomplete" ...</span></span>
<span><span class="co">#&gt; $ new_event_complete_3_follow1: chr [1:6] NA NA NA NA ...</span></span>
<span><span class="co">#&gt; $ new_event_complete_3_follow2: chr [1:6] NA NA "Incomplete" "Complete" ...</span></span></code></pre></div>
</div>
<div class="section level2">
<h2 id="creating-a-nice-table">Creating a nice table<a class="anchor" aria-label="anchor" href="#creating-a-nice-table"></a>
</h2>
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">wide_data</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">sex</span>,<span class="va">hypertension</span>, <span class="va">diabetes</span><span class="op">)</span> <span class="op">|&gt;</span> </span>
<span> <span class="fu">gtsummary</span><span class="fu">::</span><span class="fu"><a href="https://www.danieldsjoberg.com/gtsummary/reference/tbl_summary.html" class="external-link">tbl_summary</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
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border-top-color: #D3D3D3;
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border-bottom-color: #D3D3D3;
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border-left-color: #D3D3D3;
border-right-style: none;
border-right-width: 2px;
border-right-color: #D3D3D3;
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margin: 0px;
font-size: 90%;
padding-top: 4px;
padding-bottom: 4px;
padding-left: 5px;
padding-right: 5px;
}
#ulbfdpbcyv .gt_sourcenotes {
color: #333333;
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#ulbfdpbcyv div.Reactable > div.rt-table > div.rt-thead > div.rt-tr.rt-tr-group-header > div.rt-th-group:after {
height: 0px !important;
}
</style>
<table class="table gt_table" data-quarto-disable-processing="false" data-quarto-bootstrap="false">
<thead><tr class="gt_col_headings">
<th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" scope="col" id="label"><span class="gt_from_md"><strong>Characteristic</strong></span></th>
<th class="gt_col_heading gt_columns_bottom_border gt_center" rowspan="1" colspan="1" scope="col" id="stat_0">
<span class="gt_from_md"><strong>N = 6</strong></span><span class="gt_footnote_marks" style="white-space:nowrap;font-style:italic;font-weight:normal;line-height:0;"><sup>1</sup></span>
</th>
</tr></thead>
<tbody class="gt_table_body">
<tr>
<td headers="label" class="gt_row gt_left">Legal sex</td>
<td headers="stat_0" class="gt_row gt_center"><br></td>
</tr>
<tr>
<td headers="label" class="gt_row gt_left">    female</td>
<td headers="stat_0" class="gt_row gt_center">3 (50%)</td>
</tr>
<tr>
<td headers="label" class="gt_row gt_left">    male</td>
<td headers="stat_0" class="gt_row gt_center">3 (50%)</td>
</tr>
<tr>
<td headers="label" class="gt_row gt_left">Hypertension</td>
<td headers="stat_0" class="gt_row gt_center"><br></td>
</tr>
<tr>
<td headers="label" class="gt_row gt_left">    No</td>
<td headers="stat_0" class="gt_row gt_center">2 (40%)</td>
</tr>
<tr>
<td headers="label" class="gt_row gt_left">    Yes</td>
<td headers="stat_0" class="gt_row gt_center">3 (60%)</td>
</tr>
<tr>
<td headers="label" class="gt_row gt_left">    Unknown</td>
<td headers="stat_0" class="gt_row gt_center">1</td>
</tr>
<tr>
<td headers="label" class="gt_row gt_left">Diabetes</td>
<td headers="stat_0" class="gt_row gt_center"><br></td>
</tr>
<tr>
<td headers="label" class="gt_row gt_left">    No</td>
<td headers="stat_0" class="gt_row gt_center">2 (40%)</td>
</tr>
<tr>
<td headers="label" class="gt_row gt_left">    Yes</td>
<td headers="stat_0" class="gt_row gt_center">3 (60%)</td>
</tr>
<tr>
<td headers="label" class="gt_row gt_left">    Unknown</td>
<td headers="stat_0" class="gt_row gt_center">1</td>
</tr>
</tbody>
<tfoot class="gt_footnotes"><tr>
<td class="gt_footnote" colspan="2">
<span class="gt_footnote_marks" style="white-space:nowrap;font-style:italic;font-weight:normal;line-height:0;"><sup>1</sup></span> <span class="gt_from_md">n (%)</span>
</td>
</tr></tfoot>
</table>
</div>
</div>
</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
</nav></aside>

112
articles/Shiny-app.html
View File

@ -91,68 +91,65 @@ and launch the app as follows:</p>
<span> <span class="fu"><a href="../reference/redcap_wider.html">redcap_wider</a></span><span class="op">(</span><span class="op">)</span> </span>
<span><span class="co">#&gt; Joining with `by = join_by(record_id)`</span></span>
<span><span class="co">#&gt; Joining with `by = join_by(record_id)`</span></span>
<span><span class="co">#&gt; Joining with `by = join_by(record_id)`</span></span>
<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="va">ds</span><span class="op">)</span></span>
<span><span class="co">#&gt; 'data.frame': 6 obs. of 52 variables:</span></span>
<span><span class="co">#&gt; $ record_id : num 1 2 3 4 5 6</span></span>
<span><span class="co">#&gt; $ cpr : chr "1203401OB4" "0102342303" "2301569823" "0204051342" ...</span></span>
<span><span class="co">#&gt; $ inclusion : Date, format: "2023-03-13" "2023-03-01" ...</span></span>
<span><span class="co">#&gt; $ inclusion_time : 'hms' num 12:38:49 10:38:57 12:01:07 20:39:19 ...</span></span>
<span><span class="co">#&gt; tibble [6 × 49] (S3: tbl_df/tbl/data.frame)</span></span>
<span><span class="co">#&gt; $ record_id : num [1:6] 1 2 3 4 5 6</span></span>
<span><span class="co">#&gt; $ cpr : chr [1:6] "1203401OB4" "0102342303" "2301569823" "0204051342" ...</span></span>
<span><span class="co">#&gt; $ inclusion : Date[1:6], format: "2023-03-13" "2023-03-01" ...</span></span>
<span><span class="co">#&gt; $ inclusion_time : 'hms' num [1:6] 12:38:49 10:38:57 12:01:07 20:39:19 ...</span></span>
<span><span class="co">#&gt; ..- attr(*, "units")= chr "secs"</span></span>
<span><span class="co">#&gt; $ dob : Date, format: "1940-03-12" "1934-02-01" ...</span></span>
<span><span class="co">#&gt; $ age : num 83 89.1 66.1 117.9 126.2 ...</span></span>
<span><span class="co">#&gt; $ age_integer : num 83 89 66 117 126 91</span></span>
<span><span class="co">#&gt; $ sex : chr "female" "male" "male" "female" ...</span></span>
<span><span class="co">#&gt; $ cohabitation : chr "Yes" "Yes" "No" NA ...</span></span>
<span><span class="co">#&gt; $ hypertension : chr "No" "No" "Yes" NA ...</span></span>
<span><span class="co">#&gt; $ diabetes : chr "Yes" "No" "Yes" NA ...</span></span>
<span><span class="co">#&gt; $ region : chr "East" "South" "North" NA ...</span></span>
<span><span class="co">#&gt; $ baseline_data_start_complete: chr "Incomplete" "Incomplete" "Incomplete" "Incomplete" ...</span></span>
<span><span class="co">#&gt; $ mrs_assessed_inclusion : chr "Yes" "Yes" NA NA ...</span></span>
<span><span class="co">#&gt; $ mrs_assessed_follow1 : chr NA "Yes" "Yes" NA ...</span></span>
<span><span class="co">#&gt; $ mrs_assessed_follow2 : chr NA NA "Yes" NA ...</span></span>
<span><span class="co">#&gt; $ mrs_date_inclusion : Date, format: "2023-03-13" "2023-03-07" ...</span></span>
<span><span class="co">#&gt; $ mrs_date_follow1 : Date, format: NA "2023-03-09" ...</span></span>
<span><span class="co">#&gt; $ mrs_date_follow2 : Date, format: NA NA ...</span></span>
<span><span class="co">#&gt; $ mrs_score_inclusion : num 1 1 NA NA NA NA</span></span>
<span><span class="co">#&gt; $ mrs_score_follow1 : num NA 3 2 NA NA NA</span></span>
<span><span class="co">#&gt; $ mrs_score_follow2 : num NA NA 1 NA NA NA</span></span>
<span><span class="co">#&gt; $ mrs_complete_inclusion : chr "Incomplete" "Incomplete" NA NA ...</span></span>
<span><span class="co">#&gt; $ mrs_complete_follow1 : chr NA "Incomplete" "Incomplete" NA ...</span></span>
<span><span class="co">#&gt; $ mrs_complete_follow2 : chr NA NA "Incomplete" NA ...</span></span>
<span><span class="co">#&gt; $ con_mrs : logi NA NA NA NA NA NA</span></span>
<span><span class="co">#&gt; $ con_calc : logi NA NA NA NA NA NA</span></span>
<span><span class="co">#&gt; $ consensus_complete : chr NA NA NA NA ...</span></span>
<span><span class="co">#&gt; $ event_datetime_1_follow1 : POSIXct, format: NA "2024-01-18 12:49:42" ...</span></span>
<span><span class="co">#&gt; $ event_datetime_1_follow2 : POSIXct, format: NA NA ...</span></span>
<span><span class="co">#&gt; $ event_age_1_follow1 : num NA NA NA 96 127 NA</span></span>
<span><span class="co">#&gt; $ event_age_1_follow2 : num NA NA NA 118 NA NA</span></span>
<span><span class="co">#&gt; $ event_type_1_follow1 : chr NA "TIA" "AIS" "TIA" ...</span></span>
<span><span class="co">#&gt; $ event_type_1_follow2 : chr NA NA "ICH" "AIS" ...</span></span>
<span><span class="co">#&gt; $ new_event_complete_1_follow1: chr NA "Incomplete" "Incomplete" "Complete" ...</span></span>
<span><span class="co">#&gt; $ new_event_complete_1_follow2: chr NA NA "Incomplete" "Complete" ...</span></span>
<span><span class="co">#&gt; $ event_datetime_2_follow1 : POSIXct, format: NA NA ...</span></span>
<span><span class="co">#&gt; $ event_datetime_2_follow2 : POSIXct, format: NA NA ...</span></span>
<span><span class="co">#&gt; $ event_datetime_3_follow1 : POSIXct, format: NA NA ...</span></span>
<span><span class="co">#&gt; $ event_datetime_3_follow2 : POSIXct, format: NA NA ...</span></span>
<span><span class="co">#&gt; $ event_age_2_follow1 : num NA NA NA 105 127 NA</span></span>
<span><span class="co">#&gt; $ event_age_2_follow2 : num NA NA NA 118 NA NA</span></span>
<span><span class="co">#&gt; $ event_age_3_follow1 : num NA NA NA NA NA NA</span></span>
<span><span class="co">#&gt; $ event_age_3_follow2 : num NA NA NA 118 NA NA</span></span>
<span><span class="co">#&gt; $ event_type_2_follow1 : chr NA NA "ICH" "TIA" ...</span></span>
<span><span class="co">#&gt; $ event_type_2_follow2 : chr NA NA "TIA" "ICH" ...</span></span>
<span><span class="co">#&gt; $ event_type_3_follow1 : chr NA NA NA NA ...</span></span>
<span><span class="co">#&gt; $ event_type_3_follow2 : chr NA NA "AIS" "Unknown" ...</span></span>
<span><span class="co">#&gt; $ new_event_complete_2_follow1: chr NA NA "Incomplete" "Complete" ...</span></span>
<span><span class="co">#&gt; $ new_event_complete_2_follow2: chr NA NA "Incomplete" "Incomplete" ...</span></span>
<span><span class="co">#&gt; $ new_event_complete_3_follow1: chr NA NA NA NA ...</span></span>
<span><span class="co">#&gt; $ new_event_complete_3_follow2: chr NA NA "Incomplete" "Complete" ...</span></span></code></pre></div>
<span><span class="co">#&gt; $ dob : Date[1:6], format: "1940-03-12" "1934-02-01" ...</span></span>
<span><span class="co">#&gt; $ age : num [1:6] 83 89.1 66.1 117.9 126.2 ...</span></span>
<span><span class="co">#&gt; $ age_integer : num [1:6] 83 89 66 117 126 91</span></span>
<span><span class="co">#&gt; $ sex : chr [1:6] "female" "male" "male" "female" ...</span></span>
<span><span class="co">#&gt; $ cohabitation : chr [1:6] "Yes" "Yes" "No" NA ...</span></span>
<span><span class="co">#&gt; $ hypertension : chr [1:6] "No" "No" "Yes" NA ...</span></span>
<span><span class="co">#&gt; $ diabetes : chr [1:6] "Yes" "No" "Yes" NA ...</span></span>
<span><span class="co">#&gt; $ region : chr [1:6] "East" "South" "North" NA ...</span></span>
<span><span class="co">#&gt; $ baseline_data_start_complete: chr [1:6] "Incomplete" "Incomplete" "Incomplete" "Incomplete" ...</span></span>
<span><span class="co">#&gt; $ mrs_assessed_inclusion : chr [1:6] "Yes" "Yes" NA NA ...</span></span>
<span><span class="co">#&gt; $ mrs_assessed_follow1 : chr [1:6] NA "Yes" "Yes" NA ...</span></span>
<span><span class="co">#&gt; $ mrs_assessed_follow2 : chr [1:6] NA NA "Yes" NA ...</span></span>
<span><span class="co">#&gt; $ mrs_date_inclusion : Date[1:6], format: "2023-03-13" "2023-03-07" ...</span></span>
<span><span class="co">#&gt; $ mrs_date_follow1 : Date[1:6], format: NA "2023-03-09" ...</span></span>
<span><span class="co">#&gt; $ mrs_date_follow2 : Date[1:6], format: NA NA ...</span></span>
<span><span class="co">#&gt; $ mrs_score_inclusion : num [1:6] 1 1 NA NA NA NA</span></span>
<span><span class="co">#&gt; $ mrs_score_follow1 : num [1:6] NA 3 2 NA NA NA</span></span>
<span><span class="co">#&gt; $ mrs_score_follow2 : num [1:6] NA NA 1 NA NA NA</span></span>
<span><span class="co">#&gt; $ mrs_complete_inclusion : chr [1:6] "Incomplete" "Incomplete" NA NA ...</span></span>
<span><span class="co">#&gt; $ mrs_complete_follow1 : chr [1:6] NA "Incomplete" "Incomplete" NA ...</span></span>
<span><span class="co">#&gt; $ mrs_complete_follow2 : chr [1:6] NA NA "Incomplete" NA ...</span></span>
<span><span class="co">#&gt; $ event_datetime_1_follow1 : POSIXct[1:6], format: NA "2024-01-18 12:49:42" ...</span></span>
<span><span class="co">#&gt; $ event_datetime_1_follow2 : POSIXct[1:6], format: NA NA ...</span></span>
<span><span class="co">#&gt; $ event_age_1_follow1 : num [1:6] NA NA NA 96 127 NA</span></span>
<span><span class="co">#&gt; $ event_age_1_follow2 : num [1:6] NA NA NA 118 NA NA</span></span>
<span><span class="co">#&gt; $ event_type_1_follow1 : chr [1:6] NA "TIA" "AIS" "TIA" ...</span></span>
<span><span class="co">#&gt; $ event_type_1_follow2 : chr [1:6] NA NA "ICH" "AIS" ...</span></span>
<span><span class="co">#&gt; $ new_event_complete_1_follow1: chr [1:6] NA "Incomplete" "Incomplete" "Complete" ...</span></span>
<span><span class="co">#&gt; $ new_event_complete_1_follow2: chr [1:6] NA NA "Incomplete" "Complete" ...</span></span>
<span><span class="co">#&gt; $ event_datetime_2_follow1 : POSIXct[1:6], format: NA NA ...</span></span>
<span><span class="co">#&gt; $ event_datetime_2_follow2 : POSIXct[1:6], format: NA NA ...</span></span>
<span><span class="co">#&gt; $ event_datetime_3_follow1 : POSIXct[1:6], format: NA NA ...</span></span>
<span><span class="co">#&gt; $ event_datetime_3_follow2 : POSIXct[1:6], format: NA NA ...</span></span>
<span><span class="co">#&gt; $ event_age_2_follow1 : num [1:6] NA NA NA 105 127 NA</span></span>
<span><span class="co">#&gt; $ event_age_2_follow2 : num [1:6] NA NA NA 118 NA NA</span></span>
<span><span class="co">#&gt; $ event_age_3_follow1 : num [1:6] NA NA NA NA NA NA</span></span>
<span><span class="co">#&gt; $ event_age_3_follow2 : num [1:6] NA NA NA 118 NA NA</span></span>
<span><span class="co">#&gt; $ event_type_2_follow1 : chr [1:6] NA NA "ICH" "TIA" ...</span></span>
<span><span class="co">#&gt; $ event_type_2_follow2 : chr [1:6] NA NA "TIA" "ICH" ...</span></span>
<span><span class="co">#&gt; $ event_type_3_follow1 : chr [1:6] NA NA NA NA ...</span></span>
<span><span class="co">#&gt; $ event_type_3_follow2 : chr [1:6] NA NA "AIS" "Unknown" ...</span></span>
<span><span class="co">#&gt; $ new_event_complete_2_follow1: chr [1:6] NA NA "Incomplete" "Complete" ...</span></span>
<span><span class="co">#&gt; $ new_event_complete_2_follow2: chr [1:6] NA NA "Incomplete" "Incomplete" ...</span></span>
<span><span class="co">#&gt; $ new_event_complete_3_follow1: chr [1:6] NA NA NA NA ...</span></span>
<span><span class="co">#&gt; $ new_event_complete_3_follow2: chr [1:6] NA NA "Incomplete" "Complete" ...</span></span>
<span><span class="co">#&gt; - attr(*, "problems")=&lt;externalptr&gt;</span></span></code></pre></div>
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">ds</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>metadata <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="fu">REDCapCAST</span><span class="fu">::</span><span class="va"><a href="../reference/redcapcast_meta.html">redcapcast_meta</a></span><span class="op">)</span><span class="op">)</span><span class="op">|&gt;</span> </span>
<span> <span class="fu">purrr</span><span class="fu">::</span><span class="fu"><a href="https://purrr.tidyverse.org/reference/pluck.html" class="external-link">pluck</a></span><span class="op">(</span><span class="st">"data"</span><span class="op">)</span> <span class="op">|&gt;</span> </span>
<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>
<span><span class="co">#&gt; tibble [6 × 52] (S3: tbl_df/tbl/data.frame)</span></span>
<span><span class="co">#&gt; tibble [6 × 49] (S3: tbl_df/tbl/data.frame)</span></span>
<span><span class="co">#&gt; $ record_id : num [1:6] 1 2 3 4 5 6</span></span>
<span><span class="co">#&gt; $ cpr : chr [1:6] "1203401OB4" "0102342303" "2301569823" "0204051342" ...</span></span>
<span><span class="co">#&gt; $ inclusion : Date[1:6], format: "2023-03-13" "2023-03-01" ...</span></span>
@ -178,9 +175,6 @@ and launch the app as follows:</p>
<span><span class="co">#&gt; $ mrs_complete_inclusion : chr [1:6] "Incomplete" "Incomplete" NA NA ...</span></span>
<span><span class="co">#&gt; $ mrs_complete_follow1 : chr [1:6] NA "Incomplete" "Incomplete" NA ...</span></span>
<span><span class="co">#&gt; $ mrs_complete_follow2 : chr [1:6] NA NA "Incomplete" NA ...</span></span>
<span><span class="co">#&gt; $ con_mrs : Factor w/ 2 levels "FALSE","TRUE": NA NA NA NA NA NA</span></span>
<span><span class="co">#&gt; $ con_calc : Factor w/ 2 levels "FALSE","TRUE": NA NA NA NA NA NA</span></span>
<span><span class="co">#&gt; $ consensus_complete : chr [1:6] NA NA NA NA ...</span></span>
<span><span class="co">#&gt; $ event_datetime_1_follow1 : POSIXct[1:6], format: NA "2024-01-18 12:49:42" ...</span></span>
<span><span class="co">#&gt; $ event_datetime_1_follow2 : POSIXct[1:6], format: NA NA ...</span></span>
<span><span class="co">#&gt; $ event_age_1_follow1 : num [1:6] NA NA NA 96 127 NA</span></span>
@ -223,7 +217,7 @@ and launch the app as follows:</p>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> sex data <span style="color: #BB0000;">NA</span> text sex </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> cohabitation data <span style="color: #BB0000;">NA</span> text cohabitation </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> hypertension data <span style="color: #BB0000;">NA</span> text hypertension </span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 13 more variables: select_choices_or_calculations &lt;chr&gt;, field_note &lt;lgl&gt;,</span></span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 13 more variables: select_choices_or_calculations &lt;lgl&gt;, field_note &lt;lgl&gt;,</span></span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># text_validation_type_or_show_slider_number &lt;chr&gt;,</span></span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># text_validation_min &lt;lgl&gt;, text_validation_max &lt;lgl&gt;, identifier &lt;lgl&gt;,</span></span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># branching_logic &lt;lgl&gt;, required_field &lt;lgl&gt;, custom_alignment &lt;lgl&gt;,</span></span></span>

2
pkgdown.yml
View File

@ -5,7 +5,7 @@ articles:
Database-creation: Database-creation.html
REDCapCAST: REDCapCAST.html
Shiny-app: Shiny-app.html
last_built: 2024-11-27T15:00Z
last_built: 2024-11-28T13:43Z
urls:
reference: https://agdamsbo.github.io/REDCapCAST/reference
article: https://agdamsbo.github.io/REDCapCAST/articles

11
reference/REDCap_split.html
View File

@ -76,8 +76,7 @@ JSON from an API call.</p></dd>
<dt id="arg-primary-table-name">primary_table_name<a class="anchor" aria-label="anchor" href="#arg-primary-table-name"></a></dt>
<dd><p>Name given to the list element for the primary
output table (as described in <em>README.md</em>). Ignored if
<code>forms = 'all'</code>.</p></dd>
output table. Ignored if <code>forms = 'all'</code>.</p></dd>
<dt id="arg-forms">forms<a class="anchor" aria-label="anchor" href="#arg-forms"></a></dt>
@ -95,7 +94,7 @@ instruments only or for all forms.</p></dd>
</ul></div>
<div class="section level2">
<h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2>
<p>Paul W. Egeler, M.S., GStat</p>
<p>Paul W. Egeler</p>
</div>
<div class="section level2">
@ -123,7 +122,7 @@ instruments only or for all forms.</p></dd>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># Convert exported JSON strings into a list of data.frames</span></span></span>
<span class="r-in"><span><span class="fu">REDCapRITS</span><span class="fu">::</span><span class="fu">REDCap_split</span><span class="op">(</span><span class="va">records</span>, <span class="va">metadata</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="fu">REDCapCAST</span><span class="fu">::</span><span class="fu">REDCap_split</span><span class="op">(</span><span class="va">records</span>, <span class="va">metadata</span><span class="op">)</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># Using a raw data export -------------------------------------------------</span></span></span>
<span class="r-in"><span></span></span>
@ -136,7 +135,7 @@ instruments only or for all forms.</p></dd>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># Split the tables</span></span></span>
<span class="r-in"><span><span class="fu">REDCapRITS</span><span class="fu">::</span><span class="fu">REDCap_split</span><span class="op">(</span><span class="va">records</span>, <span class="va">metadata</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="fu">REDCapCAST</span><span class="fu">::</span><span class="fu">REDCap_split</span><span class="op">(</span><span class="va">records</span>, <span class="va">metadata</span><span class="op">)</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># In conjunction with the R export script ---------------------------------</span></span></span>
<span class="r-in"><span></span></span>
@ -153,7 +152,7 @@ instruments only or for all forms.</p></dd>
<span class="r-in"><span><span class="va">metadata</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/utils/read.table.html" class="external-link">read.csv</a></span><span class="op">(</span><span class="st">"ExampleProject_DataDictionary_2018-06-03.csv"</span><span class="op">)</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># Split the tables</span></span></span>
<span class="r-in"><span><span class="fu">REDCapRITS</span><span class="fu">::</span><span class="fu">REDCap_split</span><span class="op">(</span><span class="va">data</span>, <span class="va">metadata</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="fu">REDCapCAST</span><span class="fu">::</span><span class="fu">REDCap_split</span><span class="op">(</span><span class="va">data</span>, <span class="va">metadata</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/getwd.html" class="external-link">setwd</a></span><span class="op">(</span><span class="va">old</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span> <span class="co"># }</span></span></span>
</code></pre></div>

14
reference/as_factor.html
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@ -1,7 +1,7 @@
<!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"><title>Convert labelled vectors to factors while preserving attributes — as_factor • 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><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Convert labelled vectors to factors while preserving attributes — as_factor"><meta name="description" content='This extends [forcats::as_factor()] as well as [haven::as_factor()], by appending
<!-- 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"><title>Convert labelled vectors to factors while preserving attributes — as_factor • 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><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Convert labelled vectors to factors while preserving attributes — as_factor"><meta name="description" content='This extends as_factor as well as as_factor, by appending
original attributes except for "class" after converting to factor to avoid
ta loss in case of rich formatted and labelled data.'><meta property="og:description" content='This extends [forcats::as_factor()] as well as [haven::as_factor()], by appending
ta loss in case of rich formatted and labelled data.'><meta property="og:description" content='This extends as_factor as well as as_factor, by appending
original attributes except for "class" after converting to factor to avoid
ta loss in case of rich formatted and labelled data.'><meta property="og:image" content="https://agdamsbo.github.io/REDCapCAST/logo.png"></head><body>
<a href="#main" class="visually-hidden-focusable">Skip to contents</a>
@ -43,7 +43,7 @@ ta loss in case of rich formatted and labelled data.'><meta property="og:image"
</div>
<div class="ref-description section level2">
<p>This extends [forcats::as_factor()] as well as [haven::as_factor()], by appending
<p>This extends <a href="https://forcats.tidyverse.org/reference/as_factor.html" class="external-link">as_factor</a> as well as <a href="https://forcats.tidyverse.org/reference/as_factor.html" class="external-link">as_factor</a>, by appending
original attributes except for "class" after converting to factor to avoid
ta loss in case of rich formatted and labelled data.</p>
</div>
@ -80,14 +80,6 @@ ta loss in case of rich formatted and labelled data.</p>
<span> <span class="va">...</span></span>
<span><span class="op">)</span></span>
<span></span>
<span><span class="co"># S3 method for class 'redcapcast_labelled'</span></span>
<span><span class="fu">as_factor</span><span class="op">(</span></span>
<span> <span class="va">x</span>,</span>
<span> levels <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"default"</span>, <span class="st">"labels"</span>, <span class="st">"values"</span>, <span class="st">"both"</span><span class="op">)</span>,</span>
<span> ordered <span class="op">=</span> <span class="cn">FALSE</span>,</span>
<span> <span class="va">...</span></span>
<span><span class="op">)</span></span>
<span></span>
<span><span class="co"># S3 method for class 'data.frame'</span></span>
<span><span class="fu">as_factor</span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span>, only_labelled <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div>
</div>

11
reference/easy_redcap.html
View File

@ -53,7 +53,7 @@
<dl><dt id="arg-project-name">project.name<a class="anchor" aria-label="anchor" href="#arg-project-name"></a></dt>
<dd><p>The name of the current project (for key storage with
`keyring::key_set()`, using the default keyring)</p></dd>
<a href="https://keyring.r-lib.org/reference/key_get.html" class="external-link">key_set</a>, using the default keyring)</p></dd>
<dt id="arg-widen-data">widen.data<a class="anchor" aria-label="anchor" href="#arg-widen-data"></a></dt>
@ -65,7 +65,7 @@
<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
<dd><p>arguments passed on to `REDCapCAST::read_redcap_tables()`</p></dd>
<dd><p>arguments passed on to <a href="read_redcap_tables.html">read_redcap_tables</a>.</p></dd>
</dl></div>
<div class="section level2">
@ -73,6 +73,13 @@
<p>data.frame or list depending on widen.data</p>
</div>
<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="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="op">{</span> <span class="co"># \dontrun{</span></span></span>
<span class="r-in"><span><span class="fu">easy_redcap</span><span class="op">(</span><span class="st">"My_new_project"</span>,fields<span class="op">=</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"record_id"</span>,<span class="st">"age"</span>,<span class="st">"hypertension"</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span> <span class="co"># }</span></span></span>
</code></pre></div>
</div>
</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
</nav></aside></div>

23
reference/fct2num.html
View File

@ -83,23 +83,12 @@
<span class="r-in"><span> <span class="fu">fct2num</span><span class="op">(</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1 2 3 2 10 9</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># Outlier with labels, but no class of origin, handled like numeric vector</span></span></span>
<span class="r-in"><span><span class="co"># structure(c(1, 2, 3, 2, 10, 9),</span></span></span>
<span class="r-in"><span><span class="co"># labels = c(Unknown = 9, Refused = 10)</span></span></span>
<span class="r-in"><span><span class="co"># ) |&gt;</span></span></span>
<span class="r-in"><span><span class="co"># as_factor() |&gt;</span></span></span>
<span class="r-in"><span><span class="co"># fct2num()</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">v</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/sample.html" class="external-link">sample</a></span><span class="op">(</span><span class="fl">6</span><span class="op">:</span><span class="fl">19</span>, <span class="fl">20</span>, <span class="cn">TRUE</span><span class="op">)</span> <span class="op">|&gt;</span> <span class="fu"><a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a></span><span class="op">(</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/dput.html" class="external-link">dput</a></span><span class="op">(</span><span class="va">v</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> structure(c(7L, 1L, 10L, 3L, 10L, 10L, 9L, 8L, 3L, 2L, 6L, 8L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3L, 5L, 4L, 8L, 1L, 6L, 5L, 5L), levels = c("6", "7", "8", "9", </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> "11", "12", "13", "15", "16", "17"), class = "factor")</span>
<span class="r-in"><span><span class="fu"><a href="named_levels.html">named_levels</a></span><span class="op">(</span><span class="va">v</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 13 6 17 8 16 15 7 12 11 9 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1 10 3 9 8 2 6 5 4 </span>
<span class="r-in"><span><span class="fu">fct2num</span><span class="op">(</span><span class="va">v</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 13 6 17 8 17 17 16 15 8 7 12 15 8 11 9 15 6 12 11 11</span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/structure.html" class="external-link">structure</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span>, <span class="fl">2</span>, <span class="fl">3</span>, <span class="fl">2</span>, <span class="fl">10</span>, <span class="fl">9</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> labels <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>Unknown <span class="op">=</span> <span class="fl">9</span>, Refused <span class="op">=</span> <span class="fl">10</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">)</span> <span class="op">|&gt;</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="as_factor.html">as_factor</a></span><span class="op">(</span><span class="op">)</span> <span class="op">|&gt;</span></span></span>
<span class="r-in"><span> <span class="fu">fct2num</span><span class="op">(</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1 2 3 2 NA NA</span>
</code></pre></div>
</div>
</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>

100
reference/format_redcap_factor.html Normal file
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@ -0,0 +1,100 @@
<!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"><title>Converts REDCap choices to factor levels and stores in labels attribute — format_redcap_factor • 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><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Converts REDCap choices to factor levels and stores in labels attribute — format_redcap_factor"><meta name="description" content="Applying as_factor to the data.frame or variable, will
coerce to a factor."><meta property="og:description" content="Applying as_factor to the data.frame or variable, will
coerce to a factor."><meta property="og:image" content="https://agdamsbo.github.io/REDCapCAST/logo.png"></head><body>
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<main id="main" class="col-md-9"><div class="page-header">
<img src="../logo.png" class="logo" alt=""><h1>Converts REDCap choices to factor levels and stores in labels attribute</h1>
<small class="dont-index">Source: <a href="https://github.com/agdamsbo/REDCapCAST/blob/main/R/read_redcap_tables.R" class="external-link"><code>R/read_redcap_tables.R</code></a></small>
<div class="d-none name"><code>format_redcap_factor.Rd</code></div>
</div>
<div class="ref-description section level2">
<p>Applying <a href="as_factor.html">as_factor</a> to the data.frame or variable, will
coerce to a factor.</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">format_redcap_factor</span><span class="op">(</span><span class="va">data</span>, <span class="va">meta</span><span class="op">)</span></span></code></pre></div>
</div>
<div class="section level2">
<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
<dl><dt id="arg-data">data<a class="anchor" aria-label="anchor" href="#arg-data"></a></dt>
<dd><p>vector</p></dd>
<dt id="arg-meta">meta<a class="anchor" aria-label="anchor" href="#arg-meta"></a></dt>
<dd><p>vector of REDCap choices</p></dd>
</dl></div>
<div class="section level2">
<h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
<p>vector of class "labelled" with a "labels" attribute</p>
</div>
<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="fu">format_redcap_factor</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/sample.html" class="external-link">sample</a></span><span class="op">(</span><span class="fl">1</span><span class="op">:</span><span class="fl">3</span>,<span class="fl">20</span>,<span class="cn">TRUE</span><span class="op">)</span>,<span class="st">"1, First. | 2, second | 3, THIRD"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1 3 3 2 3 2 3 2 3 2 2 1 3 2 2 3 1 2 1 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> attr(,"labels")</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> First. second THIRD </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> "1" "2" "3" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> attr(,"class")</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "labelled"</span>
</code></pre></div>
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<p>Developed by Andreas Gammelgaard Damsbo, Paul Egeler.</p>
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<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
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16
reference/get_api_key.html
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@ -1,5 +1,9 @@
<!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"><title>Retrieve project API key if stored, if not, set and retrieve — get_api_key • 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><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Retrieve project API key if stored, if not, set and retrieve — get_api_key"><meta name="description" content="Retrieve project API key if stored, if not, set and retrieve"><meta property="og:description" content="Retrieve project API key if stored, if not, set and retrieve"><meta property="og:image" content="https://agdamsbo.github.io/REDCapCAST/logo.png"></head><body>
<!-- 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"><title>Retrieve project API key if stored, if not, set and retrieve — get_api_key • 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><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Retrieve project API key if stored, if not, set and retrieve — get_api_key"><meta name="description" content="Attempting to make secure API key storage so simple, that no other way makes
sense. Wrapping key_get and key_set using the
key_list to check if key is in storage already."><meta property="og:description" content="Attempting to make secure API key storage so simple, that no other way makes
sense. Wrapping key_get and key_set using the
key_list to check if key is in storage already."><meta property="og:image" content="https://agdamsbo.github.io/REDCapCAST/logo.png"></head><body>
<a href="#main" class="visually-hidden-focusable">Skip to contents</a>
@ -39,12 +43,14 @@
</div>
<div class="ref-description section level2">
<p>Retrieve project API key if stored, if not, set and retrieve</p>
<p>Attempting to make secure API key storage so simple, that no other way makes
sense. Wrapping <a href="https://keyring.r-lib.org/reference/key_get.html" class="external-link">key_get</a> and <a href="https://keyring.r-lib.org/reference/key_get.html" class="external-link">key_set</a> using the
<a href="https://keyring.r-lib.org/reference/key_get.html" class="external-link">key_list</a> to check if key is in storage already.</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">get_api_key</span><span class="op">(</span><span class="va">key.name</span><span class="op">)</span></span></code></pre></div>
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">get_api_key</span><span class="op">(</span><span class="va">key.name</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
</div>
<div class="section level2">
@ -54,6 +60,10 @@
<dl><dt id="arg-key-name">key.name<a class="anchor" aria-label="anchor" href="#arg-key-name"></a></dt>
<dd><p>character vector of key name</p></dd>
<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
<dd><p>passed to <a href="https://keyring.r-lib.org/reference/key_get.html" class="external-link">key_set</a></p></dd>
</dl></div>
<div class="section level2">
<h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>

14
reference/index.html
View File

@ -199,6 +199,12 @@
<dd>focused_metadata</dd>
</dl><dl><dt>
<code><a href="format_redcap_factor.html">format_redcap_factor()</a></code>
</dt>
<dd>Converts REDCap choices to factor levels and stores in labels attribute</dd>
</dl><dl><dt>
<code><a href="format_subheader.html">format_subheader()</a></code>
</dt>
@ -313,6 +319,12 @@
<dd>Helper to auto-parse un-formatted data with haven and readr</dd>
</dl><dl><dt>
<code><a href="possibly_numeric.html">possibly_numeric()</a></code>
</dt>
<dd>Tests if vector can be interpreted as numeric without introducing NAs by coercion</dd>
</dl><dl><dt>
<code><a href="possibly_roman.html">possibly_roman()</a></code>
</dt>
@ -370,7 +382,7 @@
<code><a href="redcap_wider.html">redcap_wider()</a></code>
</dt>
<dd>Redcap Wider</dd>
<dd>Transforms list of REDCap data.frames to a single wide data.frame</dd>
</dl><dl><dt>
<code><a href="redcapcast_data.html">redcapcast_data</a></code>

5
reference/is.labelled.html
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@ -44,10 +44,7 @@
<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">is.labelled</span><span class="op">(</span></span>
<span> <span class="va">x</span>,</span>
<span> classes <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"redcapcast_labelled"</span>, <span class="st">"haven_labelled"</span>, <span class="st">"labelled"</span><span class="op">)</span></span>
<span><span class="op">)</span></span></code></pre></div>
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">is.labelled</span><span class="op">(</span><span class="va">x</span>, classes <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"haven_labelled"</span>, <span class="st">"labelled"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
</div>
<div class="section level2">

26
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@ -44,7 +44,13 @@
<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">named_levels</span><span class="op">(</span><span class="va">data</span>, label <span class="op">=</span> <span class="st">"labels"</span>, na.label <span class="op">=</span> <span class="cn">NULL</span>, na.value <span class="op">=</span> <span class="fl">99</span><span class="op">)</span></span></code></pre></div>
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">named_levels</span><span class="op">(</span></span>
<span> <span class="va">data</span>,</span>
<span> label <span class="op">=</span> <span class="st">"labels"</span>,</span>
<span> na.label <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span> na.value <span class="op">=</span> <span class="fl">99</span>,</span>
<span> sort.numeric <span class="op">=</span> <span class="cn">TRUE</span></span>
<span><span class="op">)</span></span></code></pre></div>
</div>
<div class="section level2">
@ -67,6 +73,10 @@
<dd><p>new value for NA strings. Ignored if na.label is NULL.
Default is 99.</p></dd>
<dt id="arg-sort-numeric">sort.numeric<a class="anchor" aria-label="anchor" href="#arg-sort-numeric"></a></dt>
<dd><p>sort factor levels if levels are numeric. Default is TRUE</p></dd>
</dl></div>
<div class="section level2">
<h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
@ -75,14 +85,22 @@ Default is 99.</p></dd>
<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="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="op">{</span> <span class="co"># \dontrun{</span></span></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/structure.html" class="external-link">structure</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span>, <span class="fl">2</span>, <span class="fl">3</span>, <span class="fl">2</span>, <span class="fl">10</span>, <span class="fl">9</span><span class="op">)</span>,</span></span>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/structure.html" class="external-link">structure</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span>, <span class="fl">2</span>, <span class="fl">3</span>, <span class="fl">2</span>, <span class="fl">10</span>, <span class="fl">9</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> labels <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>Unknown <span class="op">=</span> <span class="fl">9</span>, Refused <span class="op">=</span> <span class="fl">10</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> class <span class="op">=</span> <span class="st">"haven_labelled"</span></span></span>
<span class="r-in"><span><span class="op">)</span> <span class="op">|&gt;</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="as_factor.html">as_factor</a></span><span class="op">(</span><span class="op">)</span> <span class="op">|&gt;</span></span></span>
<span class="r-in"><span> <span class="fu">named_levels</span><span class="op">(</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span> <span class="co"># }</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 2 3 Refused Unknown </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 2 3 10 9 </span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/structure.html" class="external-link">structure</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span>, <span class="fl">2</span>, <span class="fl">3</span>, <span class="fl">2</span>, <span class="fl">10</span>, <span class="fl">9</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> labels <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>Unknown <span class="op">=</span> <span class="fl">9</span>, Refused <span class="op">=</span> <span class="fl">10</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> class <span class="op">=</span> <span class="st">"labelled"</span></span></span>
<span class="r-in"><span><span class="op">)</span> <span class="op">|&gt;</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="as_factor.html">as_factor</a></span><span class="op">(</span><span class="op">)</span> <span class="op">|&gt;</span></span></span>
<span class="r-in"><span> <span class="fu">named_levels</span><span class="op">(</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 2 3 Refused Unknown </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 2 3 10 9 </span>
</code></pre></div>
</div>
</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>

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@ -0,0 +1,93 @@
<!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"><title>Tests if vector can be interpreted as numeric without introducing NAs by coercion — possibly_numeric • 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><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Tests if vector can be interpreted as numeric without introducing NAs by coercion — possibly_numeric"><meta name="description" content="Tests if vector can be interpreted as numeric without introducing NAs by
coercion"><meta property="og:description" content="Tests if vector can be interpreted as numeric without introducing NAs by
coercion"><meta property="og:image" content="https://agdamsbo.github.io/REDCapCAST/logo.png"></head><body>
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<img src="../logo.png" class="logo" alt=""><h1>Tests if vector can be interpreted as numeric without introducing NAs by coercion</h1>
<small class="dont-index">Source: <a href="https://github.com/agdamsbo/REDCapCAST/blob/main/R/as_factor.R" class="external-link"><code>R/as_factor.R</code></a></small>
<div class="d-none name"><code>possibly_numeric.Rd</code></div>
</div>
<div class="ref-description section level2">
<p>Tests if vector can be interpreted as numeric without introducing NAs by
coercion</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">possibly_numeric</span><span class="op">(</span><span class="va">data</span><span class="op">)</span></span></code></pre></div>
</div>
<div class="section level2">
<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
<dl><dt id="arg-data">data<a class="anchor" aria-label="anchor" href="#arg-data"></a></dt>
<dd><p>vector</p></dd>
</dl></div>
<div class="section level2">
<h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
<p>logical</p>
</div>
<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="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"1"</span>,<span class="st">"5"</span><span class="op">)</span> <span class="op">|&gt;</span> <span class="fu">possibly_numeric</span><span class="op">(</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] TRUE</span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"1"</span>,<span class="st">"5"</span>,<span class="st">"e"</span><span class="op">)</span> <span class="op">|&gt;</span> <span class="fu">possibly_numeric</span><span class="op">(</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] FALSE</span>
</code></pre></div>
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50
reference/read_redcap_tables.html
View File

@ -1,13 +1,17 @@
<!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"><title>Download REDCap data — read_redcap_tables • 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><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Download REDCap data — read_redcap_tables"><meta name="description" content="Implementation of REDCap_split with a focused data acquisition approach using
REDCapR::redcap_read and only downloading specified fields, forms and/or
events using the built-in focused_metadata including some clean-up.
<!-- 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"><title>Download REDCap data — read_redcap_tables • 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><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Download REDCap data — read_redcap_tables"><meta name="description" content="Implementation of passed on to REDCap_split with a focused
data acquisition approach using passed on to redcap_read and
only downloading specified fields, forms and/or events using the built-in
focused_metadata including some clean-up.
Works with classical and longitudinal projects with or without repeating
instruments."><meta property="og:description" content="Implementation of REDCap_split with a focused data acquisition approach using
REDCapR::redcap_read and only downloading specified fields, forms and/or
events using the built-in focused_metadata including some clean-up.
instruments.
Will preserve metadata in the data.frames as labels."><meta property="og:description" content="Implementation of passed on to REDCap_split with a focused
data acquisition approach using passed on to redcap_read and
only downloading specified fields, forms and/or events using the built-in
focused_metadata including some clean-up.
Works with classical and longitudinal projects with or without repeating
instruments."><meta property="og:image" content="https://agdamsbo.github.io/REDCapCAST/logo.png"></head><body>
instruments.
Will preserve metadata in the data.frames as labels."><meta property="og:image" content="https://agdamsbo.github.io/REDCapCAST/logo.png"></head><body>
<a href="#main" class="visually-hidden-focusable">Skip to contents</a>
@ -47,11 +51,13 @@ instruments."><meta property="og:image" content="https://agdamsbo.github.io/REDC
</div>
<div class="ref-description section level2">
<p>Implementation of REDCap_split with a focused data acquisition approach using
REDCapR::redcap_read and only downloading specified fields, forms and/or
events using the built-in focused_metadata including some clean-up.
<p>Implementation of passed on to <a href="REDCap_split.html">REDCap_split</a> with a focused
data acquisition approach using passed on to <a href="https://ouhscbbmc.github.io/REDCapR/reference/redcap_read.html" class="external-link">redcap_read</a> and
only downloading specified fields, forms and/or events using the built-in
focused_metadata including some clean-up.
Works with classical and longitudinal projects with or without repeating
instruments.</p>
instruments.
Will preserve metadata in the data.frames as labels.</p>
</div>
<div class="section level2">
@ -63,8 +69,9 @@ instruments.</p>
<span> fields <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span> events <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span> forms <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span> raw_or_label <span class="op">=</span> <span class="st">"label"</span>,</span>
<span> split_forms <span class="op">=</span> <span class="st">"all"</span></span>
<span> raw_or_label <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"raw"</span>, <span class="st">"label"</span>, <span class="st">"both"</span><span class="op">)</span>,</span>
<span> split_forms <span class="op">=</span> <span class="st">"all"</span>,</span>
<span> <span class="va">...</span></span>
<span><span class="op">)</span></span></code></pre></div>
</div>
@ -97,19 +104,24 @@ instruments.</p>
<dt id="arg-raw-or-label">raw_or_label<a class="anchor" aria-label="anchor" href="#arg-raw-or-label"></a></dt>
<dd><p>raw or label tags. Can be</p>
<p>* "raw": Standard [REDCapR] method to get raw values.
* "label": Standard [REDCapR] method to get label values.
<dd><p>raw or label tags. Can be "raw", "label" or "both".</p>
<p>* "raw": Standard <a href="https://ouhscbbmc.github.io/REDCapR/reference/redcap_read.html" class="external-link">redcap_read</a> method to get raw values.
* "label": Standard <a href="https://ouhscbbmc.github.io/REDCapR/reference/redcap_read.html" class="external-link">redcap_read</a> method to get label values.
* "both": Get raw values with REDCap labels applied as labels. Use
[as_factor()] to format factors with original labels and use the
[gtsummary] package to easily get beautiful tables with original labels
from REDCap. Use [fct_drop()] to drop empty levels.</p></dd>
<a href="as_factor.html">as_factor</a> to format factors with original labels and use
the `gtsummary` package functions like <a href="https://www.danieldsjoberg.com/gtsummary/reference/tbl_summary.html" class="external-link">tbl_summary</a> to
easily get beautiful tables with original labels from REDCap. Use
<a href="fct_drop.html">fct_drop</a> to drop empty levels.</p></dd>
<dt id="arg-split-forms">split_forms<a class="anchor" aria-label="anchor" href="#arg-split-forms"></a></dt>
<dd><p>Whether to split "repeating" or "all" forms, default is
all.</p></dd>
<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
<dd><p>passed on to <a href="https://ouhscbbmc.github.io/REDCapR/reference/redcap_read.html" class="external-link">redcap_read</a></p></dd>
</dl></div>
<div class="section level2">
<h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>

43
reference/redcap_wider.html
View File

@ -1,7 +1,11 @@
<!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"><title>Redcap Wider — redcap_wider • 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><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Redcap Wider — redcap_wider"><meta name="description" content="Converts a list of REDCap data frames from long to wide format.
Handles longitudinal projects, but not yet repeated instruments."><meta property="og:description" content="Converts a list of REDCap data frames from long to wide format.
Handles longitudinal projects, but not yet repeated instruments."><meta property="og:image" content="https://agdamsbo.github.io/REDCapCAST/logo.png"></head><body>
<!-- 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"><title>Transforms list of REDCap data.frames to a single wide data.frame — redcap_wider • 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><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Transforms list of REDCap data.frames to a single wide data.frame — redcap_wider"><meta name="description" content="Converts a list of REDCap data.frames from long to wide format.
In essence it is a wrapper for the pivot_wider function applied
on a REDCap output (from read_redcap_tables) or manually
split by REDCap_split."><meta property="og:description" content="Converts a list of REDCap data.frames from long to wide format.
In essence it is a wrapper for the pivot_wider function applied
on a REDCap output (from read_redcap_tables) or manually
split by REDCap_split."><meta property="og:image" content="https://agdamsbo.github.io/REDCapCAST/logo.png"></head><body>
<a href="#main" class="visually-hidden-focusable">Skip to contents</a>
@ -35,14 +39,16 @@ Handles longitudinal projects, but not yet repeated instruments."><meta property
</nav><div class="container template-reference-topic">
<div class="row">
<main id="main" class="col-md-9"><div class="page-header">
<img src="../logo.png" class="logo" alt=""><h1>Redcap Wider</h1>
<img src="../logo.png" class="logo" alt=""><h1>Transforms list of REDCap data.frames to a single wide data.frame</h1>
<small class="dont-index">Source: <a href="https://github.com/agdamsbo/REDCapCAST/blob/main/R/redcap_wider.R" class="external-link"><code>R/redcap_wider.R</code></a></small>
<div class="d-none name"><code>redcap_wider.Rd</code></div>
</div>
<div class="ref-description section level2">
<p>Converts a list of REDCap data frames from long to wide format.
Handles longitudinal projects, but not yet repeated instruments.</p>
<p>Converts a list of REDCap data.frames from long to wide format.
In essence it is a wrapper for the <a href="https://tidyr.tidyverse.org/reference/pivot_wider.html" class="external-link">pivot_wider</a> function applied
on a REDCap output (from <a href="read_redcap_tables.html">read_redcap_tables</a>) or manually
split by <a href="REDCap_split.html">REDCap_split</a>.</p>
</div>
<div class="section level2">
@ -59,20 +65,20 @@ Handles longitudinal projects, but not yet repeated instruments.</p>
<dl><dt id="arg-data">data<a class="anchor" aria-label="anchor" href="#arg-data"></a></dt>
<dd><p>A list of data frames.</p></dd>
<dd><p>A list of data frames</p></dd>
<dt id="arg-event-glue">event.glue<a class="anchor" aria-label="anchor" href="#arg-event-glue"></a></dt>
<dd><p>A dplyr::glue string for repeated events naming</p></dd>
<dd><p>A <a href="https://glue.tidyverse.org/reference/glue.html" class="external-link">glue</a> string for repeated events naming</p></dd>
<dt id="arg-inst-glue">inst.glue<a class="anchor" aria-label="anchor" href="#arg-inst-glue"></a></dt>
<dd><p>A dplyr::glue string for repeated instruments naming</p></dd>
<dd><p>A <a href="https://glue.tidyverse.org/reference/glue.html" class="external-link">glue</a> string for repeated instruments naming</p></dd>
</dl></div>
<div class="section level2">
<h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
<p>The list of data frames in wide format.</p>
<p>data.frame in wide format</p>
</div>
<div class="section level2">
@ -92,9 +98,11 @@ Handles longitudinal projects, but not yet repeated instruments.</p>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="fu">redcap_wider</span><span class="op">(</span><span class="va">list1</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Joining with `by = join_by(record_id)`</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 2 × 4</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> record_id age_baseline age_followup gender</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1 25 27 male</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 2 26 28 female</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 1 25 27 male </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2 26 28 female</span>
<span class="r-in"><span><span class="co"># Simpel with two instruments</span></span></span>
<span class="r-in"><span><span class="va">list2</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
@ -146,12 +154,13 @@ Handles longitudinal projects, but not yet repeated instruments.</p>
<span class="r-in"><span><span class="fu">redcap_wider</span><span class="op">(</span><span class="va">list4</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Joining with `by = join_by(record_id)`</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Joining with `by = join_by(record_id)`</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 2 × 8</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> record_id age_baseline age_followup dist_1_baseline dist_1_followup</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1 25 27 40 25</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 2 26 28 28 23</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> dist_2_baseline dist_2_followup gender</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 32 33 male</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 24 36 female</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 1 25 27 40 25</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2 26 28 28 23</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 3 more variables: dist_2_baseline &lt;dbl&gt;, dist_2_followup &lt;dbl&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># gender &lt;chr&gt;</span></span>
</code></pre></div>
</div>
</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>

13
reference/sanitize_split.html
View File

@ -47,7 +47,9 @@
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">sanitize_split</span><span class="op">(</span></span>
<span> <span class="va">l</span>,</span>
<span> generic.names <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"redcap_event_name"</span>, <span class="st">"redcap_repeat_instrument"</span>,</span>
<span> <span class="st">"redcap_repeat_instance"</span><span class="op">)</span></span>
<span> <span class="st">"redcap_repeat_instance"</span><span class="op">)</span>,</span>
<span> drop.complete <span class="op">=</span> <span class="cn">TRUE</span>,</span>
<span> drop.empty <span class="op">=</span> <span class="cn">TRUE</span></span>
<span><span class="op">)</span></span></code></pre></div>
</div>
@ -62,6 +64,15 @@
<dt id="arg-generic-names">generic.names<a class="anchor" aria-label="anchor" href="#arg-generic-names"></a></dt>
<dd><p>A vector of generic names to be excluded.</p></dd>
<dt id="arg-drop-complete">drop.complete<a class="anchor" aria-label="anchor" href="#arg-drop-complete"></a></dt>
<dd><p>logical to remove genric REDCap variables indicating
instrument completion. Default is TRUE.</p></dd>
<dt id="arg-drop-empty">drop.empty<a class="anchor" aria-label="anchor" href="#arg-drop-empty"></a></dt>
<dd><p>logical to remove variables with only NAs Default is TRUE.</p></dd>
</dl></div>
<div class="section level2">
<h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>

6
reference/var2fct.html
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@ -73,15 +73,15 @@ factoring, but levels character vectors in order of appearance.</p>
<span class="r-in"><span> <span class="fu">var2fct</span><span class="op">(</span><span class="fl">6</span><span class="op">)</span> <span class="op">|&gt;</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 2 3 4 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 2 6 3 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 3 6 4 </span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/sample.html" class="external-link">sample</a></span><span class="op">(</span><span class="va">letters</span>, <span class="fl">20</span><span class="op">)</span> <span class="op">|&gt;</span></span></span>
<span class="r-in"><span> <span class="fu">var2fct</span><span class="op">(</span><span class="fl">6</span><span class="op">)</span> <span class="op">|&gt;</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Length Class Mode </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 20 character character </span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/sample.html" class="external-link">sample</a></span><span class="op">(</span><span class="va">letters</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">4</span><span class="op">]</span>, <span class="fl">20</span>, <span class="cn">TRUE</span><span class="op">)</span> <span class="op">|&gt;</span> <span class="fu">var2fct</span><span class="op">(</span><span class="fl">6</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] c d c d a b d a d c a d a c c a b c d c</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Levels: c d a b</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] a c c a b c d c c b d b a d d c b d b a</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Levels: a c b d</span>
</code></pre></div>
</div>
</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>

2
search.json
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2
sitemap.xml
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@ -35,6 +35,7 @@
<url><loc>https://agdamsbo.github.io/REDCapCAST/reference/fct_drop.html</loc></url>
<url><loc>https://agdamsbo.github.io/REDCapCAST/reference/file_extension.html</loc></url>
<url><loc>https://agdamsbo.github.io/REDCapCAST/reference/focused_metadata.html</loc></url>
<url><loc>https://agdamsbo.github.io/REDCapCAST/reference/format_redcap_factor.html</loc></url>
<url><loc>https://agdamsbo.github.io/REDCapCAST/reference/format_subheader.html</loc></url>
<url><loc>https://agdamsbo.github.io/REDCapCAST/reference/get_api_key.html</loc></url>
<url><loc>https://agdamsbo.github.io/REDCapCAST/reference/get_attr.html</loc></url>
@ -55,6 +56,7 @@
<url><loc>https://agdamsbo.github.io/REDCapCAST/reference/nav_bar_page.html</loc></url>
<url><loc>https://agdamsbo.github.io/REDCapCAST/reference/numchar2fct.html</loc></url>
<url><loc>https://agdamsbo.github.io/REDCapCAST/reference/parse_data.html</loc></url>
<url><loc>https://agdamsbo.github.io/REDCapCAST/reference/possibly_numeric.html</loc></url>
<url><loc>https://agdamsbo.github.io/REDCapCAST/reference/possibly_roman.html</loc></url>
<url><loc>https://agdamsbo.github.io/REDCapCAST/reference/process_user_input.character.html</loc></url>
<url><loc>https://agdamsbo.github.io/REDCapCAST/reference/process_user_input.data.frame.html</loc></url>